diff --git a/communities/all/resources/tools.html b/communities/all/resources/tools.html
index bd02614c..a5b98116 100644
--- a/communities/all/resources/tools.html
+++ b/communities/all/resources/tools.html
@@ -87,6 +87,7 @@
| Number of tools on CIRM-CFBP |
Number of tools on ChemFlow |
Number of tools on Coloc-stats |
+ Number of tools on CorGAT |
Number of tools on CoralSNP |
Number of tools on CropGalaxy |
Number of tools on Dintor |
@@ -100,7 +101,6 @@
Number of tools on IPK Galaxy Blast Suite |
Number of tools on ImmPort Galaxy |
Number of tools on InteractoMIX |
- Number of tools on Lebanese University Galaxy |
Number of tools on MISSISSIPPI |
Number of tools on Mandoiu Lab |
Number of tools on MiModD NacreousMap |
@@ -614,8 +614,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -806,7 +806,7 @@
https://github.com/askomics/askoR |
0.2 |
bioconductor-limma |
- 3.58.1 |
+ 3.62.0 |
To update |
Transcriptomics |
|
@@ -910,8 +910,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -1132,8 +1132,8 @@
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0 |
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1 |
0 |
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0 |
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0 |
0 |
0 |
- 20 |
0 |
+ 20 |
0 |
0 |
0 |
@@ -3248,8 +3248,8 @@
https://github.com/phac-nml/ecoli_serotyping |
1.0.0 |
ectyper |
- 1.0.0 |
- Up-to-date |
+ 2.0.0 |
+ To update |
Sequence Analysis |
|
|
@@ -3278,8 +3278,8 @@
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0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
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1 |
0 |
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0 |
0 |
- 0 |
|
@@ -8354,7 +8354,7 @@
|
1.0 |
bioconductor-preprocesscore |
- 1.64.0 |
+ 1.68.0 |
To update |
Computational chemistry |
|
@@ -8976,8 +8976,8 @@
0 |
0 |
0 |
- 12 |
0 |
+ 12 |
0 |
0 |
0 |
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1 |
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- 0 |
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@@ -15525,30 +15525,29 @@
|
- augustus |
- augustus |
- AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. |
- 2015-02-28 |
- http://bioinf.uni-greifswald.de/augustus/ |
- 3.1.0 |
- augustus |
- 3.5.0 |
- To update |
+ bamhash |
+ bamhash |
+ Hash BAM and FASTQ files to verify data integrity |
+ 2015-09-17 |
+ https://github.com/DecodeGenetics/BamHash |
+ 1.1 |
+ bamhash |
+ 1.1 |
+ Up-to-date |
Sequence Analysis |
|
|
|
|
bgruening |
- https://github.com/bgruening/galaxytools/tree/master/tools/augustus |
- https://github.com/bgruening/galaxytools/tree/master/tools/augustus |
+ https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
+ https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
|
|
|
|
- 1 |
- 1 |
- 1 |
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1 |
0 |
0 |
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0 |
0 |
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- 1 |
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0 |
0 |
@@ -15576,53 +15573,55 @@
0 |
0 |
0 |
- 1 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
1 |
1 |
0 |
- 1378 |
- 1509 |
- 10109 |
- 11052 |
- 2206 |
- 2206 |
- 12573 |
- 12573 |
- 369 |
- 369 |
- 5274 |
- 5274 |
- 3953 |
- 11990 |
- 27956 |
- 84811 |
+ 40 |
+ 44 |
+ 158 |
+ 181 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ 0 |
+ 40 |
+ 124 |
+ 158 |
+ 497 |
|
- bamhash |
- bamhash |
- Hash BAM and FASTQ files to verify data integrity |
- 2015-09-17 |
- https://github.com/DecodeGenetics/BamHash |
- 1.1 |
- bamhash |
- 1.1 |
- Up-to-date |
- Sequence Analysis |
+ barcode_collapse |
+ barcode_collapse |
+ Paired End randomer aware duplicate removal algorithm |
+ 2016-06-11 |
+ https://github.com/YeoLab/gscripts |
+ 0.1.0 |
+ pysam |
+ 0.22.1 |
+ To update |
+ RNA, Sequence Analysis |
|
|
|
|
- bgruening |
- https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
- https://github.com/bgruening/galaxytools/tree/master/tools/bamhash |
+ rnateam |
+ https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
+ https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
|
|
|
|
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0 |
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0 |
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+
+
+ |
+ basecoverage |
+ gops_basecoverage_1 |
+ Base Coverage of all intervals |
+ 2014-04-01 |
+ https://github.com/galaxyproject/gops |
+ 1.0.0 |
+ bx-python |
+ 0.13.0 |
+ To update |
+ Genomic Interval Operations |
+ |
+ |
+ |
+ |
+ devteam |
+ https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage |
+ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage |
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1 |
0 |
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- 44 |
- 158 |
- 181 |
0 |
0 |
0 |
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- 158 |
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+ 1 |
+ 1 |
+ 1 |
+ 0 |
+ 27 |
+ 35 |
+ 226 |
+ 308 |
+ 302 |
+ 2284 |
+ 2615 |
+ 45557 |
+ 32 |
+ 36 |
+ 482 |
+ 522 |
+ 361 |
+ 3077 |
+ 3323 |
+ 53033 |
|
- barcode_collapse |
- barcode_collapse |
- Paired End randomer aware duplicate removal algorithm |
- 2016-06-11 |
- https://github.com/YeoLab/gscripts |
- 0.1.0 |
- pysam |
- 0.22.1 |
+ best_regression_subsets |
+ BestSubsetsRegression1 |
+ Perform Best-subsets Regression |
+ 2014-04-01 |
+ |
+ 1.0.0 |
+ numpy |
+ |
To update |
- RNA, Sequence Analysis |
+ Sequence Analysis, Variant Analysis |
|
|
|
|
- rnateam |
- https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
- https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse |
+ devteam |
+ https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets |
+ https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets |
|
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-
- |
- basecoverage |
- gops_basecoverage_1 |
- Base Coverage of all intervals |
- 2014-04-01 |
- https://github.com/galaxyproject/gops |
- 1.0.0 |
- bx-python |
- 0.13.0 |
- To update |
- Genomic Interval Operations |
- |
- |
- |
- |
- devteam |
- https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage |
- https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage |
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- 1 |
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- 27 |
- 35 |
- 226 |
- 308 |
- 302 |
- 2284 |
- 2615 |
- 45557 |
- 32 |
- 36 |
- 482 |
- 522 |
- 361 |
- 3077 |
- 3323 |
- 53033 |
-
-
- |
- best_regression_subsets |
- BestSubsetsRegression1 |
- Perform Best-subsets Regression |
- 2014-04-01 |
- |
- 1.0.0 |
- numpy |
- |
- To update |
- Sequence Analysis, Variant Analysis |
- |
- |
- |
- |
- devteam |
- https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets |
- https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets |
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GNU diff tool that calculates the differences between two files. |
2020-03-29 |
http://www.gnu.org/software/diffutils/ |
- 3.7 |
+ 3.10 |
diffutils |
|
To update |
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https://jbrowse.org |
2.17.0 |
jbrowse2 |
- 2.17.0 |
- Up-to-date |
+ 2.18.0 |
+ To update |
Sequence Analysis |
Genome visualisation, Structure visualisation, Pathway visualisation |
Genome visualisation, Structure visualisation, Pathway visualisation |
@@ -26661,8 +26587,8 @@
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@@ -29600,7 +29526,7 @@
|
|
bgruening |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ |
+ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution |
https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution |
music_deconvolution |
MuSiC Deconvolution |
@@ -29770,8 +29696,8 @@
0 |
0 |
0 |
- 2 |
0 |
+ 2 |
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- 2015-10-16 |
- |
- 0.4.0 |
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- 1.70 |
- To update |
- Text Manipulation |
- |
- |
- |
- |
- rnateam |
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- 2018-07-05 |
- https://github.molgen.mpg.de/heller/ssHMM |
- 1.0.7 |
- sshmm |
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+ Split a multi-sequence fasta file into files containing single sequences |
+ 2015-10-16 |
+ |
+ 0.4.0 |
+ biopython |
+ 1.70 |
+ To update |
+ Text Manipulation |
+ |
+ |
+ |
+ |
+ rnateam |
+ https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta |
+ https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta |
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+
+
+ |
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+ ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data |
+ 2018-07-05 |
+ https://github.molgen.mpg.de/heller/ssHMM |
+ 1.0.7 |
+ sshmm |
+ 1.0.7 |
+ Up-to-date |
+ Sequence Analysis, RNA |
+ |
+ |
+ |
+ |
+ rnateam |
+ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ |
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+ suitable for boolean classification problems |
+ 2015-02-28 |
+ http://osmot.cs.cornell.edu/kddcup/software.html |
+ 5.11.0 |
+ perf |
+ |
+ To update |
+ |
+ |
+ |
+ |
+ |
+ bgruening |
+ https://github.com/bgruening/galaxytools/tree/master/tools/perf |
+ https://github.com/bgruening/galaxytools/tree/master/tools/perf |
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171 |
4314 |
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+ |
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+ A little word cloud generator in Python. |
+ 2024-12-13 |
+ https://github.com/amueller/word_cloud |
+ 1.9.4 |
+ wordcloud |
+ |
+ To update |
+ Visualization |
+ |
+ |
+ |
+ |
+ bgruening |
+ https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud |
+ https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud |
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https://github.com/xiezhq/ISEScan |
1.7.2.3 |
isescan |
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- To update |
+ 1.7.2.3 |
+ Up-to-date |
Sequence Analysis |
Structural variation detection |
Structural variation detection |
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https://github.com/FrederickHuangLin/ANCOMBC |
1.4.0 |
bioconductor-ancombc |
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+ 2.8.0 |
To update |
Metagenomics |
DNA barcoding |
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1.9.4 |
bakta |
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To update |
Sequence Analysis |
Genome annotation |
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1150 |
3450 |
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+ |
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+ ete_treeviewer |
+ A toolkit for the analysis and visualization of trees. |
+ 2024-11-25 |
+ http://etetoolkit.org |
+ 3.1.3 |
+ curl |
+ |
+ To update |
+ Phylogenetics |
+ Phylogenetic analysis, Phylogenetic tree editing |
+ Phylogenetic tree editing |
+ Phylogenetics |
+ Phylogenetics |
+ iuc |
+ https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit |
+ ete |
+ ete |
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2.0.6 |
subread |
- 2.0.6 |
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+ To update |
RNA, Transcriptomics, Sequence Analysis |
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Sequence Analysis |
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https://github.com/PacificBiosciences/pbmm2 |
1.16.0 |
pbmm2 |
- 1.16.0 |
- Up-to-date |
+ 1.16.99 |
+ To update |
Next Gen Mappers |
Pairwise sequence alignment, Sorting |
Pairwise sequence alignment, Sorting |
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167 |
167 |
1902 |
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Proteinortho is a tool to detect orthologous proteins/genes within different species. |
2020-02-05 |
https://gitlab.com/paulklemm_PHD/proteinortho |
- 6.3.1 |
+ 6.3.4 |
proteinortho |
- 6.3.3 |
- To update |
+ 6.3.4 |
+ Up-to-date |
Proteomics |
Sequence clustering, Sequence analysis |
Sequence clustering, Sequence analysis |
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|
qiime |
- 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 |
+ qiime_collapse_samples, qiime_make_otu_table |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
@@ -69487,15 +69635,14 @@
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core |
- qiime_core |
- qiime_core |
- QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on |
+ qiime_add_on |
+ qiime_add_on |
+ QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
|
0 |
0 |
- 32 |
- 32 |
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- 10550 |
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+ 210 |
+ 659 |
+ 2094 |
+ 6532 |
|
qiime |
- qiime_collapse_samples, qiime_make_otu_table |
+ 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 |
QIIME to perform microbial community analysis |
2017-01-16 |
http://www.qiime.org |
@@ -69561,18 +69709,14 @@
Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics |
iuc |
https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on |
- qiime_add_on |
- qiime_add_on |
- QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core |
+ qiime_core |
+ qiime_core |
+ QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. |
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0 |
0 |
0 |
@@ -78005,7 +78153,7 @@
2 |
0 |
2 |
- 2 |
+ 0 |
0 |
0 |
0 |
@@ -78079,7 +78227,8 @@
1 |
1 |
1 |
- 1 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -78105,7 +78254,6 @@
0 |
0 |
0 |
- 0 |
1 |
1 |
1 |
@@ -78227,7 +78375,6 @@
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0 |
1 |
- 1 |
0 |
0 |
0 |
@@ -78240,9 +78387,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -78301,7 +78449,8 @@
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1 |
1 |
- 1 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -78320,7 +78469,6 @@
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0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -78462,8 +78610,8 @@
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0 |
0 |
- 1 |
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+ 1 |
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0 |
0 |
@@ -78523,7 +78671,6 @@
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5 |
5 |
- 5 |
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0 |
0 |
@@ -78536,9 +78683,10 @@
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0 |
- 5 |
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0 |
+ 5 |
+ 0 |
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0 |
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1 |
- 1 |
+ 0 |
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0 |
0 |
@@ -78654,8 +78802,8 @@
http://bioconductor.org/packages/tximport/ |
1.30.0 |
bioconductor-tximport |
- 1.30.0 |
- Up-to-date |
+ 1.34.0 |
+ To update |
Transcriptomics |
Pathway or network analysis, Formatting, RNA-Seq analysis |
Pathway or network analysis, Formatting, RNA-Seq analysis |
@@ -79189,7 +79337,6 @@
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1 |
1 |
- 1 |
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0 |
0 |
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0 |
0 |
@@ -79800,7 +79949,6 @@
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- 0 |
1 |
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0 |
@@ -79929,7 +80077,6 @@
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0 |
@@ -79942,9 +80089,10 @@
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0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80225,7 +80373,6 @@
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3 |
3 |
- 3 |
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0 |
0 |
@@ -80238,9 +80385,10 @@
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0 |
- 1 |
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0 |
+ 1 |
+ 0 |
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0 |
0 |
@@ -80385,8 +80533,8 @@
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0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -80447,7 +80595,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80460,9 +80607,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80521,7 +80669,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80534,9 +80681,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80595,7 +80743,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80608,9 +80755,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80743,7 +80891,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80756,9 +80903,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80817,7 +80965,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80830,9 +80977,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80891,7 +81039,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80904,9 +81051,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -80965,7 +81113,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -80978,9 +81125,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81039,7 +81187,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81052,9 +81199,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81113,7 +81261,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81126,9 +81273,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81187,7 +81335,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81200,9 +81347,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81261,7 +81409,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81274,9 +81421,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81335,7 +81483,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81348,9 +81495,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81409,7 +81557,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81422,9 +81569,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81483,7 +81631,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81496,9 +81643,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81557,7 +81705,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81570,9 +81717,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81631,7 +81779,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81644,9 +81791,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81705,7 +81853,6 @@
1 |
1 |
1 |
- 1 |
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0 |
0 |
@@ -81718,9 +81865,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
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0 |
0 |
@@ -81779,7 +81927,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81792,9 +81939,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81853,7 +82001,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -81866,9 +82013,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -81927,7 +82075,6 @@
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1 |
1 |
- 1 |
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0 |
0 |
@@ -81940,9 +82087,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -82001,7 +82149,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -82014,9 +82161,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -82075,7 +82223,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -82088,9 +82235,10 @@
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0 |
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- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -82149,7 +82297,6 @@
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1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -82162,9 +82309,10 @@
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0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -82297,7 +82445,8 @@
2 |
2 |
2 |
- 2 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -82323,7 +82472,6 @@
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0 |
0 |
- 0 |
2 |
2 |
0 |
@@ -82382,6 +82530,7 @@
0 |
0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -82397,7 +82546,6 @@
0 |
0 |
0 |
- 0 |
1 |
1 |
1 |
@@ -82519,7 +82667,7 @@
0 |
0 |
3 |
- 3 |
+ 0 |
0 |
0 |
0 |
@@ -82741,7 +82889,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -82752,10 +82899,11 @@
0 |
0 |
0 |
- 1 |
+ 0 |
0 |
1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -82815,7 +82963,8 @@
8 |
8 |
8 |
- 8 |
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+ 0 |
0 |
0 |
0 |
@@ -82834,7 +82983,6 @@
0 |
0 |
0 |
- 0 |
8 |
0 |
0 |
@@ -82963,7 +83111,6 @@
1 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -82974,9 +83121,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -83390,7 +83538,7 @@
https://github.com/artic-network/fieldbioinformatics |
|
artic |
- 1.5.7 |
+ 1.5.8 |
To update |
Sequence Analysis |
Sequence alignment |
@@ -83420,8 +83568,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -83716,8 +83864,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
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0 |
0 |
@@ -83789,8 +83937,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -83925,7 +84073,8 @@
3 |
3 |
3 |
- 3 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -83944,7 +84093,6 @@
0 |
0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -84073,7 +84221,7 @@
3 |
5 |
5 |
- 5 |
+ 0 |
0 |
0 |
0 |
@@ -84147,7 +84295,8 @@
5 |
5 |
5 |
- 5 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -84166,7 +84315,6 @@
0 |
0 |
0 |
- 0 |
3 |
0 |
0 |
@@ -84295,7 +84443,6 @@
2 |
2 |
2 |
- 2 |
0 |
0 |
0 |
@@ -84308,9 +84455,10 @@
0 |
0 |
0 |
- 2 |
0 |
0 |
+ 2 |
+ 0 |
0 |
0 |
0 |
@@ -84443,16 +84591,16 @@
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0 |
0 |
- 1 |
0 |
0 |
0 |
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -84591,7 +84739,8 @@
0 |
12 |
12 |
- 12 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -84617,7 +84766,6 @@
0 |
0 |
0 |
- 0 |
12 |
12 |
12 |
@@ -84665,7 +84813,7 @@
17 |
2 |
17 |
- 2 |
+ 0 |
0 |
0 |
0 |
@@ -84739,7 +84887,8 @@
2 |
2 |
2 |
- 2 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -84765,7 +84914,6 @@
0 |
0 |
0 |
- 0 |
2 |
2 |
2 |
@@ -84813,7 +84961,6 @@
5 |
5 |
5 |
- 4 |
0 |
0 |
0 |
@@ -84826,9 +84973,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -84887,7 +85035,6 @@
3 |
5 |
5 |
- 5 |
0 |
0 |
0 |
@@ -84899,9 +85046,10 @@
0 |
0 |
0 |
- 5 |
0 |
0 |
+ 5 |
+ 0 |
0 |
0 |
0 |
@@ -84961,7 +85109,6 @@
2 |
2 |
2 |
- 2 |
0 |
0 |
0 |
@@ -84974,9 +85121,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -85035,7 +85183,6 @@
2 |
2 |
2 |
- 2 |
0 |
0 |
0 |
@@ -85048,9 +85195,10 @@
0 |
0 |
0 |
- 2 |
0 |
0 |
+ 2 |
+ 0 |
0 |
0 |
0 |
@@ -85109,7 +85257,6 @@
3 |
3 |
3 |
- 3 |
0 |
0 |
0 |
@@ -85122,9 +85269,10 @@
0 |
0 |
0 |
- 3 |
0 |
0 |
+ 3 |
+ 0 |
0 |
0 |
0 |
@@ -85257,7 +85405,7 @@
2 |
0 |
2 |
- 2 |
+ 0 |
0 |
0 |
0 |
@@ -85405,7 +85553,6 @@
1 |
1 |
2 |
- 2 |
0 |
0 |
0 |
@@ -85418,9 +85565,10 @@
0 |
0 |
0 |
- 2 |
0 |
0 |
+ 2 |
+ 0 |
0 |
0 |
0 |
@@ -85479,7 +85627,7 @@
1 |
1 |
1 |
- 1 |
+ 0 |
0 |
0 |
0 |
@@ -85553,7 +85701,7 @@
0 |
0 |
2 |
- 2 |
+ 0 |
0 |
0 |
0 |
@@ -85714,8 +85862,8 @@
0 |
0 |
0 |
- 13 |
0 |
+ 13 |
0 |
0 |
0 |
@@ -85775,7 +85923,7 @@
0 |
0 |
0 |
- 1 |
+ 0 |
0 |
0 |
0 |
@@ -85849,7 +85997,8 @@
3 |
3 |
3 |
- 1 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -85868,7 +86017,6 @@
0 |
0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -85914,7 +86062,7 @@
Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression |
Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression |
iuc |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 |
+ https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid |
https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid |
RaceID |
RaceID |
@@ -85923,7 +86071,7 @@
5 |
5 |
5 |
- 1 |
+ 0 |
0 |
0 |
0 |
@@ -85997,7 +86145,6 @@
0 |
1 |
1 |
- 1 |
0 |
0 |
0 |
@@ -86010,9 +86157,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -86071,7 +86219,6 @@
2 |
0 |
2 |
- 2 |
0 |
0 |
0 |
@@ -86084,9 +86231,10 @@
0 |
0 |
0 |
- 2 |
0 |
0 |
+ 2 |
+ 0 |
0 |
0 |
0 |
@@ -86515,7 +86663,7 @@
0 |
12 |
12 |
- 12 |
+ 0 |
0 |
0 |
0 |
@@ -86589,7 +86737,7 @@
0 |
0 |
1 |
- 1 |
+ 0 |
0 |
0 |
0 |
@@ -86811,7 +86959,8 @@
9 |
13 |
13 |
- 13 |
+ 0 |
+ 0 |
0 |
0 |
0 |
@@ -86830,7 +86979,6 @@
0 |
0 |
0 |
- 0 |
11 |
0 |
0 |
@@ -86885,7 +87033,7 @@
0 |
0 |
1 |
- 1 |
+ 0 |
0 |
0 |
0 |
@@ -86942,8 +87090,8 @@
https://github.com/CGATOxford/UMI-tools |
1.1.5 |
umi_tools |
- 1.1.5 |
- Up-to-date |
+ 1.1.6 |
+ To update |
Sequence Analysis, Transcriptomics, Single Cell |
Sequencing quality control |
Sequencing quality control |
@@ -86959,7 +87107,6 @@
5 |
5 |
5 |
- 5 |
0 |
0 |
0 |
@@ -86972,9 +87119,10 @@
0 |
0 |
0 |
- 1 |
0 |
0 |
+ 1 |
+ 0 |
0 |
0 |
0 |
@@ -87046,8 +87194,8 @@
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0 |
0 |
- 3 |
0 |
+ 3 |
0 |
0 |
0 |
@@ -87107,7 +87255,7 @@
0 |
0 |
3 |
- 3 |
+ 0 |
0 |
0 |
0 |
@@ -87194,8 +87342,8 @@
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0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -87858,8 +88006,8 @@
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0 |
0 |
- 2 |
0 |
+ 2 |
0 |
0 |
0 |
@@ -88525,8 +88673,8 @@
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0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -88672,8 +88820,8 @@
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0 |
0 |
- 5 |
0 |
+ 5 |
0 |
0 |
0 |
@@ -89044,8 +89192,8 @@
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0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -89118,8 +89266,8 @@
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0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -89191,6 +89339,7 @@
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0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -89198,7 +89347,6 @@
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0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -89266,8 +89414,8 @@
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0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -89339,6 +89487,7 @@
0 |
0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -89346,7 +89495,6 @@
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0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -89414,8 +89562,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -89487,8 +89635,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -89783,6 +89931,7 @@
0 |
0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -89790,7 +89939,6 @@
0 |
0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -90079,6 +90227,7 @@
0 |
0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -90086,7 +90235,6 @@
1 |
0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -90228,8 +90376,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -90302,8 +90450,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -90524,8 +90672,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -92448,8 +92596,8 @@
0 |
0 |
0 |
- 1 |
0 |
+ 1 |
0 |
0 |
0 |
@@ -92891,6 +93039,7 @@
0 |
0 |
0 |
+ 0 |
1 |
1 |
0 |
@@ -92898,7 +93047,6 @@
0 |
0 |
0 |
- 0 |
1 |
0 |
0 |
@@ -93380,7 +93528,7 @@
http://artbio.fr |
2.32.0+galaxy0 |
bioconductor-qvalue |
- 2.34.0 |
+ 2.38.0 |
To update |
RNA, Statistics |
|
@@ -93705,6 +93853,7 @@
0 |
0 |
0 |
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18 |
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3332 |
9996 |
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+ |
+ max_projections_stack_and_upload_omero |
+ max_projections_stack_and_upload_omero |
+ Combine images from max projections to stack and upload to the omero server |
+ 2024-12-12 |
+ |
+ 20241213.2 |
+ Fiji |
+ 20240614 |
+ To update |
+ Imaging |
+ |
+ |
+ |
+ |
+ lldelisle |
+ https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero |
+ https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero |
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md_converter |
- md_slicer |
- A tool for slicing trajectory files using MDTraj. |
- 2019-10-07 |
+ md_converter |
+ A tool for interconverting between different MD structure and trajectory file formats. |
+ 2018-10-13 |
|
- 1.9.9 |
+ 1.9.7 |
mdtraj |
|
To update |
@@ -96866,8 +97088,8 @@
|
|
chemteam |
- https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer |
- https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer |
+ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter |
+ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter |
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|
md_converter |
- md_converter |
- A tool for interconverting between different MD structure and trajectory file formats. |
- 2018-10-13 |
+ md_slicer |
+ A tool for slicing trajectory files using MDTraj. |
+ 2019-10-07 |
|
- 1.9.7 |
+ 1.9.9 |
mdtraj |
|
To update |
@@ -96940,8 +97162,8 @@
|
|
chemteam |
- https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter |
- https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter |
+ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer |
+ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer |
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https://github.com/galaxyproteomics/tools-galaxyp/ |
0.1.19 |
bioconductor-preprocesscore |
- 1.64.0 |
+ 1.68.0 |
To update |
Proteomics |
|
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https:// |
1.40.0 |
bioconductor-pathifier |
- 1.40.0 |
- Up-to-date |
+ 1.44.0 |
+ To update |
Transcriptomics, Statistics |
|
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uniprotxml_downloader |
Download UniProt proteome in XML or fasta format |
2016-03-08 |
- |
- 2.4.0 |
+ https://www.uniprot.org/help/programmatic_access |
+ 2.5.0 |
requests |
|
To update |
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https://github.com/MeenaChoi/MSstats |
4.0.0 |
bioconductor-msstats |
- 4.10.0 |
+ 4.14.0 |
To update |
Proteomics |
Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling |
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diff --git a/communities/all/resources/tools.json b/communities/all/resources/tools.json
index 07cb9649..389bdaa3 100644
--- a/communities/all/resources/tools.json
+++ b/communities/all/resources/tools.json
@@ -9,7 +9,7 @@
"Homepage": "https://github.com/askomics/askoR",
"Suite version": "0.2",
"Suite conda package": "bioconductor-limma",
- "Latest suite conda package version": "3.58.1",
+ "Latest suite conda package version": "3.62.0",
"Suite version status": "To update",
"ToolShed categories": [
"Transcriptomics"
@@ -34,6 +34,7 @@
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"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
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"Number of tools on Dintor": 0,
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"Number of tools on InteractoMIX": 0,
- "Number of tools on Lebanese University Galaxy": 0,
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@@ -121897,6 +122145,7 @@
"Number of tools on CIRM-CFBP": 0,
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"Number of tools on CoralSNP": 0,
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@@ -121910,7 +122159,6 @@
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@@ -121987,6 +122235,7 @@
"Number of tools on CIRM-CFBP": 0,
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+ "Number of tools on CorGAT": 0,
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@@ -122000,7 +122249,6 @@
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@@ -122081,6 +122329,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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"Number of tools on Dintor": 0,
@@ -122094,7 +122343,6 @@
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"Number of tools on MISSISSIPPI": 16,
"Number of tools on Mandoiu Lab": 0,
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@@ -122201,6 +122449,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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@@ -122214,7 +122463,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
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@@ -122296,6 +122544,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122309,7 +122558,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
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@@ -122383,6 +122631,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
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+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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"Number of tools on Dintor": 0,
@@ -122396,7 +122645,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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@@ -122464,6 +122712,7 @@
"Number of tools on CIRM-CFBP": 0,
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+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122477,7 +122726,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
"Number of tools on Mandoiu Lab": 0,
"Number of tools on MiModD NacreousMap": 0,
@@ -122541,6 +122789,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122554,7 +122803,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
"Number of tools on Mandoiu Lab": 0,
"Number of tools on MiModD NacreousMap": 0,
@@ -122633,6 +122881,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122646,7 +122895,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
"Number of tools on ImmPort Galaxy": 0,
"Number of tools on InteractoMIX": 0,
- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
"Number of tools on Mandoiu Lab": 0,
"Number of tools on MiModD NacreousMap": 0,
@@ -122736,6 +122984,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122749,7 +122998,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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"Number of tools on InteractoMIX": 0,
- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
"Number of tools on Mandoiu Lab": 0,
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@@ -122813,6 +123061,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122826,7 +123075,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
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"Number of tools on Mandoiu Lab": 0,
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@@ -122891,6 +123139,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122904,7 +123153,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
"Number of tools on Mandoiu Lab": 0,
"Number of tools on MiModD NacreousMap": 0,
@@ -122968,6 +123216,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -122981,7 +123230,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
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@@ -123065,6 +123313,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
"Number of tools on CropGalaxy": 0,
"Number of tools on Dintor": 0,
@@ -123078,7 +123327,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
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@@ -123150,6 +123398,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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"Number of tools on Dintor": 0,
@@ -123163,7 +123412,6 @@
"Number of tools on IPK Galaxy Blast Suite": 0,
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- "Number of tools on Lebanese University Galaxy": 0,
"Number of tools on MISSISSIPPI": 0,
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@@ -123227,6 +123475,7 @@
"Number of tools on CIRM-CFBP": 0,
"Number of tools on ChemFlow": 0,
"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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@@ -123240,7 +123489,6 @@
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- "Number of tools on Lebanese University Galaxy": 0,
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@@ -123306,6 +123554,7 @@
"Number of tools on CIRM-CFBP": 0,
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"Number of tools on Coloc-stats": 0,
+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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@@ -123319,7 +123568,6 @@
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@@ -123383,6 +123631,7 @@
"Number of tools on CIRM-CFBP": 0,
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+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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@@ -123396,7 +123645,6 @@
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@@ -123460,6 +123708,7 @@
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@@ -123473,7 +123722,6 @@
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@@ -123537,6 +123785,7 @@
"Number of tools on CIRM-CFBP": 0,
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+ "Number of tools on CorGAT": 0,
"Number of tools on CoralSNP": 0,
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@@ -123550,7 +123799,6 @@
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diff --git a/communities/all/resources/tools.tsv b/communities/all/resources/tools.tsv
index 696d7912..37979651 100644
--- a/communities/all/resources/tools.tsv
+++ b/communities/all/resources/tools.tsv
@@ -1,18 +1,18 @@
-Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on ARGs-OAP Number of tools on CIRM-CFBP Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on Lebanese University Galaxy Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) on main servers Suite users on main servers Suite runs (last 5 years) on main servers Suite runs on main servers
+Suite ID Tool IDs Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on ARGs-OAP Number of tools on CIRM-CFBP Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CorGAT Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) on main servers Suite users on main servers Suite runs (last 5 years) on main servers Suite runs on main servers
2d_auto_threshold ip_threshold Automatic thresholding 2019-01-22 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 120 122 1434 6746 0 0 0 0 11 11 305 305 131 395 1739 10529
2d_feature_extraction ip_2d_feature_extraction 2D feature extraction 2019-01-08 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 42 1156 13842 0 0 0 0 4 4 121 121 44 134 1277 16517
2d_filter_segmentation_by_features ip_2d_filter_segmentation_by_features filter segmentation by rules 2019-07-19 https://github.com/bmcv 0.0.1-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 38 40 591 6863 0 0 0 0 3 3 119 119 41 125 710 8402
2d_histogram_equalization ip_histogram_equalization 2d histogram equalization 2019-07-23 https://github.com/bmcv 0.18.1 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 100 101 762 782 0 0 0 0 14 14 230 230 114 343 992 2996
2d_simple_filter ip_filter_standard 2d simple filter 2019-01-22 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter scipy 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 98 100 948 6261 0 0 0 0 13 13 153 153 111 335 1101 8616
2dnmrannotation 2DNmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra 2020-02-04 http://workflow4metabolomics.org 2.0.0 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-abacas abacas Order and Orientate Contigs 2019-11-20 https://github.com/phac-nml/abacas 1.1 mummer 3.23 To update Assembly nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+abacas abacas Order and Orientate Contigs 2019-11-20 https://github.com/phac-nml/abacas 1.1 mummer 3.23 To update Assembly nml https://github.com/phac-nml/abacas https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
anisotropic_diffusion ip_anisotropic_diffusion Anisotropic image diffusion 2018-12-04 https://github.com/bmcv 0.4.0 medpy 0.4.0 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 36 41 0 0 0 0 0 0 0 0 2 6 36 113
apoc apoc Large-scale structural comparison of protein pockets 2017-07-04 http://cssb.biology.gatech.edu/APoc 1.0+galaxy1 apoc 1b16 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 4 4 1 1 1 1 0 0 0 0 5 15 5 15
-askor_de askor_de AskoR links EdgeR and AskOmics 2018-04-06 https://github.com/askomics/askoR 0.2 bioconductor-limma 3.58.1 To update Transcriptomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+askor_de askor_de AskoR links EdgeR and AskOmics 2018-04-06 https://github.com/askomics/askoR 0.2 bioconductor-limma 3.62.0 To update Transcriptomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/askor https://github.com/genouest/galaxy-tools/tree/master/tools/askor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+assemblystats assemblystats Summarise an assembly (e.g. N50 metrics) 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
background_removal background_removal Background removal filters using scikit-image 2024-07-12 https://github.com/bmcv 0.24.0 scikit-image To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tools/background_removal https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 5 5 0 0 0 0 0 0 0 0 1 3 5 15
bam2mappingstats bam2mappingstats Generates mapping stats from a bam file. 2017-10-13 https://github.com/phac-nml/galaxy_tools 1.1.0 perl To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. 2020-04-28 https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 Up-to-date Sequence Analysis nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+bamclipper bamclipper Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format. 2020-04-28 https://github.com/tommyau/bamclipper 1.0.0 bamclipper 1.0.0 Up-to-date Sequence Analysis nml https://github.com/tommyau/bamclipper https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
batched_lastz batched_lastz Galaxy wrapper for the batching Lastz runs 2024-04-30 https://github.com/galaxyproject/KegAlign 1.04.22 lastz 1.04.22 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 123 123 0 0 0 0 5 15 123 369
bfconvert ip_convertimage Convert image 2019-07-22 https://github.com/bmcv 6.7.0 bftools 8.0.0 To update Imaging, Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert python-bioformats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 123 124 1635 1671 0 0 0 0 21 21 334 334 144 433 1969 5943
binary2labelimage ip_binary_to_labelimage Binary 2 label image 2017-02-11 https://github.com/bmcv 0.5 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 87 88 401 1385 0 0 0 0 9 9 188 188 96 289 589 2751
@@ -23,10 +23,10 @@ biohansel_bionumeric_converter bionumeric_convert Convert BioHansel output data
blast_parser blast_parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 2015-08-06 https://github.com/TGAC/earlham-galaxytools/ 0.1.2 To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 99 104 417 438 0 0 0 0 0 0 0 0 99 302 417 1272
braker braker BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 2021-10-05 https://github.com/Gaius-Augustus/BRAKER 2.1.6 To update Genome annotation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 48 48 165 165 0 0 0 0 0 0 0 0 48 144 165 495
braker3 braker3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes . 2023-06-13 https://github.com/Gaius-Augustus/BRAKER 3.0.8 To update Genome annotation Genome annotation, Gene prediction Genome annotation, Gene prediction RNA-Seq, Genomics, Structure prediction, Sequence analysis RNA-Seq, Genomics, Structure prediction, Sequence analysis genouest https://github.com/genouest/galaxy-tools/tree/master/tools/braker https://github.com/genouest/galaxy-tools/tree/master/tools/braker3 braker3 BRAKER3 BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 294 294 1938 1938 0 0 0 0 71 71 412 412 365 1095 2350 7050
-bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download 2015-11-20 1.3.0 perl-getopt-long 2.58 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 73 76 1518 1526 74 225 1520 4568
+bundle_collections bundle_collection Tool to bundle up list collection into a single zip to be download 2015-11-20 1.3.0 perl-getopt-long 2.58 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 2 2 73 76 1518 1526 74 225 1520 4568
camera abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos, CAMERA_findAdducts, CAMERA_findIsotopes, CAMERA_groupCorr, CAMERA_groupFWHM 2023-05-25 1.48.0 r-snow 0.4_1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera 1 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 114 120 677 787 30 30 60 60 26 26 734 746 170 516 1471 4535
cfmid cfmid Competitive Fragmentation Modeling (CFM) 2019-03-07 https://sourceforge.net/p/cfm-id/ 33 cfm 33 Up-to-date Metabolomics computational-metabolomics https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-collapse_collections collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection 2015-12-10 5.1.0 gawk To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3555 3629 39518 40471 3536 4045 22007 24841 814 835 3969 4101 7905 24319 65494 200401
+collapse_collections collapse_dataset Collection tool that collapses a list of files into a single datasset in order of appears in collection 2015-12-10 5.1.0 gawk To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3555 3629 39518 40471 3536 4045 22007 24841 814 835 3969 4101 7905 24319 65494 200401
color_deconvolution ip_color_deconvolution Color-deconvolution methods 2024-09-30 https://github.com/bmcv 0.8 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 15 16 0 0 0 0 0 0 0 0 2 7 15 46
colorize_labels colorize_labels Colorize label map 2024-03-12 https://github.com/bmcv 3.2.1 networkx To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 40 40 0 0 0 0 0 0 0 0 2 6 40 120
combine_assemblystats combine_stats Combine multiple Assemblystats datasets into a single tabular report 2017-11-08 https://github.com/phac-nml/galaxy_tools 1.0 perl-getopt-long 2.58 To update Assembly nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -38,10 +38,10 @@ coordinates_of_roi ip_coordinates_of_roi Coordinates of ROI 2019-01-08 https://g
correlation_analysis correlation_analysis [Metabolomics][W4M] Metabolites Correlation Analysis 2020-12-08 http://workflow4metabolomics.org 1.0.1+galaxy0 r-batch 1.1_4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
count_objects ip_count_objects Count Objects 2019-01-08 https://github.com/bmcv 0.0.5-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 73 75 314 326 0 0 0 0 6 6 129 129 79 239 443 1341
cryptogenotyper CryptoGenotyper CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. 2020-10-14 https://github.com/phac-nml/CryptoGenotyper 1.0 cryptogenotyper 1.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/CryptoGenotyper https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 26 26 9942 9942 0 0 0 0 0 0 0 0 26 78 9942 29826
-csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files 2019-08-23 https://bioinf.shenwei.me/csvtk/ 0.20.0 csvtk 0.31.0 To update Text Manipulation nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+csvtk csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq Rapid data investigation and manipulation of csv/tsv files 2019-08-23 https://bioinf.shenwei.me/csvtk/ 0.20.0 csvtk 0.31.0 To update Text Manipulation nml https://github.com/shenwei356/csvtk https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
curve_fitting ip_curve_fitting Polynomial curve fitting to data points 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 12 12 0 0 0 0 0 0 0 0 2 6 12 36
detection_viz ip_detection_viz Detection Visualization 2017-10-30 https://github.com/bmcv 0.3-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 8 8 43 48 0 0 0 0 0 0 0 0 8 24 43 134
-ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping 1.0.0 ectyper 1.0.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 137 137 12996 12996 1 1 10 10 0 0 0 0 138 414 13006 39018
+ectyper ectyper EC-Typer - in silico serotyping of Escherichia coli species 2018-12-21 https://github.com/phac-nml/ecoli_serotyping 1.0.0 ectyper 2.0.0 To update Sequence Analysis nml https://github.com/phac-nml/ecoli_serotyping https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 137 137 12996 12996 1 1 10 10 0 0 0 0 138 414 13006 39018
ete ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator Analyse phylogenetic trees using the ETE Toolkit 2016-06-01 http://etetoolkit.org/ 3.1.2 ete3 3.1.1 To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete ete ete 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 0 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 0 89 106 820 966 0 0 0 0 0 0 0 0 89 284 820 2606
export_to_cluster export_to_cluster Export datasets to cluster 2016-01-18 https://github.com/TGAC/earlham-galaxytools/ 0.0.2 EXPORT_DIR_PREFIX To update Data Export earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fasta2bed fasta2bed Convert multiple fasta file into tabular bed file format 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -49,14 +49,14 @@ fasta_extract fa-extract-sequence extract single fasta from multiple fasta file
fastqc_stats FastQC_Summary Summary multiple FastQC into a single tabular line report 2017-10-11 https://github.com/phac-nml/galaxy_tools 1.2 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feelnc2asko feelnc2asko Convert FeelNC GTF to GFF3 2018-04-11 https://github.com/tderrien/FEELnc 0.1 perl-bioperl 1.7.8 To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feht feht Automatically identify makers predictive of groups. 2017-10-11 https://github.com/phac-nml/galaxy_tools 0.1.0 feht 1.1.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds 2017-10-12 https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+filter_spades_repeats filter_spades_repeat Remove short and repeat contigs/scaffolds 2017-10-12 https://github.com/phac-nml/galaxy_tools/ 1.0.1 perl-bioperl 1.7.8 To update Assembly nml https://github.com/phac-nml/galaxy_tools/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gafa gafa Gene Align and Family Aggregator 2016-12-15 http://aequatus.tgac.ac.uk 0.3.1 To update Visualization earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 6 40 47 0 0 0 0 0 0 0 0 6 18 40 127
-gblocks gblocks Gblocks 2018-04-11 http://molevol.cmima.csic.es/castresana/Gblocks.html 0.91b gblocks 0.91b Up-to-date Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 62 62 466 466 62 186 466 1398
+gblocks gblocks Gblocks 2018-04-11 http://molevol.cmima.csic.es/castresana/Gblocks.html 0.91b gblocks 0.91b Up-to-date Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 62 62 466 466 62 186 466 1398
gcms2isocor gcms2isocor Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs 2023-03-15 https://github.com/p2m2/p2m2tools 0.2.1 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gcms2isocor gcms2isocor Conversion from GCMS PostRun Analysis to Isocor 2021-09-16 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
genform genform genform: generation of molecular formulas by high-resolution MS and MS/MS data 2019-09-12 https://sourceforge.net/projects/genform/ genform r8 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/ https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 68 68 0 0 0 0 0 0 0 0 4 12 68 204
get_pairs get_pairs Separate paired and unpaired reads from two fastq files 2018-09-10 0.3 python To update Fastq Manipulation genouest https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-getmlst getmlst Download MLST datasets by species from pubmlst.org 2015-12-03 0.1.4.1 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+getmlst getmlst Download MLST datasets by species from pubmlst.org 2015-12-03 0.1.4.1 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gnali gnali A tool to find nonessential, loss-of-function gene variants 2020-03-30 https://github.com/phac-nml/gnali/ 1.1.0 gnali 1.1.0 Up-to-date Variant Analysis nml https://github.com/phac-nml/gnali/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gstf_preparation gstf_preparation GeneSeqToFamily preparation converts data for the workflow 2017-03-15 https://github.com/TGAC/earlham-galaxytools/ 0.4.3 python To update Convert Formats earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 17 377 400 0 0 0 0 0 0 0 0 17 51 377 1154
hcluster_sg hcluster_sg Hierarchically clustering on a sparse graph 2015-08-05 https://github.com/douglasgscofield/hcluster 0.5.1.1 hcluster_sg 0.5.1 To update Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 54 57 243 263 0 0 0 0 0 0 0 0 54 165 243 749
@@ -88,29 +88,29 @@ mergeneighboursinlabelimage ip_merge_neighbours_in_label Merge Neighbours in Lab
miranda miranda Finds potential target sites for miRNAs in genomic sequences 2015-10-30 http://www.microrna.org/ 3.3a+galaxy1 miranda 3.3a To update RNA earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 99 6408 6514 0 0 0 0 0 0 0 0 94 287 6408 19330
miranda2asko miranda2asko Converts miRanda output into AskOmics format 2018-04-12 0.2 perl To update Convert Formats genouest https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mixmodel4repeated_measures mixmodel4repeated_measures [Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model 2022-05-16 http://workflow4metabolomics.org 3.1.0 r-lme4 To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.0.3 mob_suite 3.1.9 To update Sequence Analysis nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 628 628 119024 119024 2 2 42 42 191 191 36310 36310 821 2463 155376 466128
+mob_suite mob_recon, mob_typer MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies 2018-04-30 https://github.com/phac-nml/mob-suite 3.0.3 mob_suite 3.1.9 To update Sequence Analysis nml https://github.com/phac-nml/mob-suite https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 628 628 119024 119024 2 2 42 42 191 191 36310 36310 821 2463 155376 466128
morphological_operations morphological_operations Apply morphological operations to images 2024-03-08 https://github.com/bmcv 1.12.0 scipy To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations scipy 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-mrbayes mrbayes A program for the Bayesian estimation of phylogeny. 2015-12-04 1.0.2 mrbayes 3.2.7 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+mrbayes mrbayes A program for the Bayesian estimation of phylogeny. 2015-12-04 1.0.2 mrbayes 3.2.7 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ms2snoop ms2snoop [W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity. 2022-03-15 http://workflow4metabolomics.org 2.2.1 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mykrobe_parser mykrobe_parseR RScript to parse the results of mykrobe predictor. 2018-09-28 https://github.com/phac-nml/mykrobe-parser 0.1.4.1 r-base To update Sequence Analysis nml https://github.com/phac-nml/mykrobe-parser https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzxmlshaper mzxmlshaper Convert mzML, mzXML or netCDF files to mzML or mzXML 2024-09-20 https://rdrr.io/bioc/mzR/ 1.0.0+galaxy0 r-base To update Metabolomics workflow4metabolomics https://github.com/workflow4metabolomics/tools-metabolomics https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ncbi_egapx ncbi_egapx Eukaryotic Genome Annotation Pipeline - External (EGAPx) 2024-08-19 https://github.com/ncbi/egapx 0.2-alpha To update Genome annotation richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 15 15 0 0 0 0 6 18 15 45
-ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. 2024-02-23 https://github.com/ncbi/fcs 0.5.0 To update Sequence Analysis richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 93 842 842 0 0 0 0 93 279 842 2526
+ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. 2024-02-23 https://github.com/ncbi/fcs 0.5.0 To update Sequence Analysis richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 93 842 842 0 0 0 0 93 279 842 2526
nmr_annotation NmrAnnotation [Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation 2019-07-30 http://workflow4metabolomics.org 3.0.0 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_annotation https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 49 49 0 0 0 0 0 0 0 0 5 15 49 147
nmr_preprocessing NMR_Preprocessing, NMR_Read [Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction 2019-07-29 http://workflow4metabolomics.org r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/nmr_preprocessing https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 8 8 142 142 0 0 0 0 9 9 335 341 17 51 477 1437
normalization normalization [Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data 2019-07-30 http://workflow4metabolomics.org 1.0.7 r-batch 1.1_4 To update Metabolomics marie-tremblay-metatoul https://github.com/workflow4metabolomics/normalization https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 40 152 162 0 0 0 0 12 12 233 236 51 154 385 1168
openlabcds2csv openlabcds2csv "Creates a summary of several ""Internal Standard Report"" OpenLabCDS results." 2021-10-28 0.1.0 openjdk To update Metabolomics genouest https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
orientationpy orientationpy Compute image orientation 2024-03-12 https://github.com/bmcv 0.2.0.4 orientationpy 0.2.0.4 Up-to-date Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy orientationj 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
overlay_images ip_overlay_images Overlay two images 2022-02-26 https://github.com/BMCV/galaxy-image-analysis 0.0.4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 31 31 149 149 0 0 0 0 1 1 18 18 32 96 167 501
-pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages 2020-05-01 https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3.1 To update Sequence Analysis nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 508 508 7457 7457 377 377 8518 8518 259 259 2760 2760 1144 3432 18735 56205
+pangolin pangolin Phylogenetic Assignment of Named Global Outbreak LINeages 2020-05-01 https://github.com/hCoV-2019/pangolin 1.1.14 pangolin 4.3.1 To update Sequence Analysis nml https://github.com/hCoV-2019/pangolin https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 508 508 7457 7457 377 377 8518 8518 259 259 2760 2760 1144 3432 18735 56205
patrist patrist Extract Patristic Distance From a Tree 2019-12-14 https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02 0.1.2 python To update Phylogenetics nml https://github.com/phac-nml/patrist https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
permutate_axis ip_permutate_axis Permutates axes 2017-10-30 https://github.com/bmcv 0.2-2 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 2 36 42 0 0 0 0 0 0 0 0 1 4 36 114
physiofit physiofit PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes 2022-09-26 physiofit.readthedocs.io 3.4.0 physiofit 3.4.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaSys-LISBP/PhysioFit https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
physiofit_manager physiofit_data_manager Handling of physiofit input files 2022-11-03 physiofit.readthedocs.io 1.0.1 physiofit_data_manager 1.0.1 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
plantseg plantseg Tool for cell instance aware segmentation in densely packed 3D volumetric images 2024-06-19 https://github.com/bmcv 1.8.1 plant-seg To update Imaging Network analysis, Quantification, Microscope image visualisation Network analysis, Quantification, Microscope image visualisation Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg plantseg PlantSeg Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-plasmid_profiler plasmid_profiler Explores plasmid content in WGS data 2016-11-07 0.1.6 r To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-plasmidspades plasmidspades Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.0.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. 2017-07-04 1.0 bioconductor-preprocesscore 1.64.0 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+plasmid_profiler plasmid_profiler Explores plasmid content in WGS data 2016-11-07 0.1.6 r To update nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+plasmidspades plasmidspades Genome assembler for assemblying plasmid 2016-06-06 1.1 spades 4.0.0 To update Assembly nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+plotheatmap plotheatmap This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output. 2017-07-04 1.0 bioconductor-preprocesscore 1.68.0 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pneumocat pneumocat Pneumococcal Capsular Typing of illumina fastq reads 2020-03-24 https://github.com/phe-bioinformatics/PneumoCaT 1.2.1 pneumocat 1.2.1 Up-to-date Variant Analysis nml https://github.com/phe-bioinformatics/PneumoCaT https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
points2labelimage ip_points_to_label Points to label image 2017-10-30 https://github.com/bmcv 0.4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 2 33 33 0 0 0 0 0 0 0 0 2 6 33 99
points_association_nn ip_points_association_nn Association of points in consecutive frames 2021-07-22 https://github.com/BMCV/galaxy-image-analysis 0.0.3-2 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 29 29 0 0 0 0 0 0 0 0 4 12 29 87
@@ -118,9 +118,9 @@ projective_transformation ip_projective_transformation Projective transformation
projective_transformation_points ip_projective_transformation_points Projective transformation of ROIs defined by pixel (point) coordinates 2018-12-07 https://github.com/bmcv 0.1.1 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 14 18 20858 21444 0 0 0 0 0 0 0 0 14 46 20858 63160
promer promer4_substitutions Aligns two sets of contigs and reports amino acid substitutions between them 2019-12-14 https://github.com/phac-nml/promer 1.2 python To update Assembly nml https://github.com/phac-nml/promer https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pseudogenome pseudogenome Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters. 2018-04-06 https://github.com/phac-nml/galaxy_tools 1.0.0 perl-bioperl 1.7.8 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies 2017-10-05 https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 434 434 13483 13483 434 1302 13483 40449
+quasitools aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality A collection of tools for analysing Viral Quasispecies 2017-10-05 https://github.com/phac-nml/quasitools 0.7.0 quasitools 0.7.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/quasitools https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools 0 12 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 434 434 13483 13483 434 1302 13483 40449
rdock rdock Docking ligands to proteins and nucleic acids 2016-12-14 http://rdock.sourceforge.net/ 1.0 rDock 2013.1 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. 2018-01-31 https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 2 0 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 428 428 42 42 141 141 0 0 0 0 77 231 569 1707
+refseq_masher refseq_masher_contains, refseq_masher_matches Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database. 2018-01-31 https://github.com/phac-nml/refseq_masher 0.1.2 refseq_masher 0.1.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/refseq_masher https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 35 428 428 42 42 141 141 0 0 0 0 77 231 569 1707
repeat_channels repeat_channels Convert single-channel to multi-channel image 2024-04-25 https://github.com/bmcv 1.26.4 numpy To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 5 5 0 0 0 0 0 0 0 0 1 3 5 15
repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. 2023-11-01 https://github.com/repeatexplorer/repex_tarean 2.3.8 To update Genome annotation gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 38 95 95 0 0 0 0 0 0 0 0 38 114 95 285
replace_chromosome_names replace_chromosome_names Replace chromosome names 2017-05-18 0.1 python To update Text Manipulation earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 69 83 514 573 0 0 0 0 0 0 0 0 69 221 514 1601
@@ -130,10 +130,10 @@ scale_image ip_scale_image Scale image 2018-12-07 https://github.com/bmcv 0.18.3
segalign segalign A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm. 2024-04-15 https://github.com/gsneha26/SegAlign 0.1.2.7 segalign-galaxy 0.1.2.7 Up-to-date Next Gen Mappers richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47 47 252 252 0 0 0 0 47 141 252 756
segmetrics ip_segmetrics Image segmentation and object detection performance measures 2022-10-07 https://github.com/bmcv 1.4 segmetrics 1.5 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics segmetrics SegMetrics Image segmentation and object detection performance measures segmetrics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 7 7 0 0 0 0 0 0 0 0 2 6 7 21
seqtk_nml seqtk_nml_sample Tool to downsample fastq reads 2017-09-19 https://github.com/lh3/seqtk 1.0.1 seqtk 1.4 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-sistr_cmd sistr_cmd SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd 1.1.1 sistr_cmd 1.1.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 301 301 3457 3457 0 0 0 0 65 65 556 556 366 1098 4013 12039
+sistr_cmd sistr_cmd SISTR in silico serotyping tool 2017-02-20 https://github.com/phac-nml/sistr_cmd 1.1.1 sistr_cmd 1.1.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 301 301 3457 3457 0 0 0 0 65 65 556 556 366 1098 4013 12039
skyline2isocor skyline2isocor Converting skyline output to IsoCor input 2024-02-07 https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor 1.0.0 skyline2isocor 1.0.0 Up-to-date Metabolomics workflow4metabolomics https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
slice_image ip_slice_image Slice image 2017-10-30 https://github.com/bmcv 0.3-4 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 5 96 103 0 0 0 0 1 1 4 4 5 16 100 307
-smalt smalt SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 0.7.6 smalt 0.7.6 Up-to-date Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+smalt smalt SMALT aligns DNA sequencing reads with a reference genome. 2017-09-19 http://www.sanger.ac.uk/science/tools/smalt-0 0.7.6 smalt 0.7.6 Up-to-date Sequence Analysis nml https://sourceforge.net/projects/smalt/ https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smart_domains smart_domains SMART domains 2017-05-12 http://smart.embl.de/ 0.1.0 perl-bioperl 1.7.8 To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smina smina smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization 2017-07-07 https://sourceforge.net/projects/smina/ 1.0 smina 2017.11.9 To update Computational chemistry earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 16 499 499 10 10 44 44 0 0 0 0 26 78 543 1629
spades_fasta_header_fixer spades_header_fixer Fixes Spades Fasta ids 2019-12-18 https://github.com/phac-nml/galaxy_tools 1.1.2+galaxy1 sed To update Fasta Manipulation nml https://github.com/phac-nml/galaxy_tools https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -141,15 +141,15 @@ spatyper spatyper Determines SPA type based on repeats in a submitted staphyloco
split_labelmap ip_split_labelmap Split Labelmaps 2018-12-11 https://github.com/bmcv 0.2-3 scikit-image To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 3 44 51 0 0 0 0 0 0 0 0 2 7 44 139
spolpred spolpred A program for predicting the spoligotype from raw sequence reads 2015-12-14 1.0.1 spolpred To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spot_detection_2d ip_spot_detection_2d Spot detection in 2D image sequence 2021-07-20 https://github.com/BMCV/galaxy-image-analysis 0.1 giatools 0.3.1 To update Imaging Image analysis Image analysis Imaging, Bioinformatics Imaging, Bioinformatics imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d galaxy_image_analysis Galaxy Image Analysis Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 16 16 0 0 0 0 0 0 0 0 4 12 16 48
-srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 297 297 1 1 71 71 0 0 0 0 41 123 368 1104
-staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2018-05-10 https://github.com/phac-nml/staramr 0.10.0 staramr 0.10.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2030 2045 20778 20891 1424 1424 9520 9520 864 864 6753 6753 4318 12969 37051 111266
-stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 2015-12-02 0.3.7 srst2 0.2.0 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 297 297 1 1 71 71 0 0 0 0 41 123 368 1104
+staramr staramr_search Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2018-05-10 https://github.com/phac-nml/staramr 0.10.0 staramr 0.10.0 Up-to-date Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2030 2045 20778 20891 1424 1424 9520 9520 864 864 6753 6753 4318 12969 37051 111266
+stringmlst stringmlst Rapid and accurate identification of the sequence type (ST) 2016-10-19 1.1.0 stringMLST 0.6.3 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_plasmid_profiler Plasmid Profiler suite defining all dependencies for Plasmid Profiler 2016-11-07 To update Sequence Analysis nml https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
superdsm ip_superdsm Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images 2023-06-20 https://github.com/bmcv 0.2.0 superdsm 0.4.0 To update Imaging Image analysis Image analysis imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm superdsm SuperDSM SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond. superdsm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 26 26 0 0 0 0 0 0 0 0 5 15 26 78
t_coffee t_coffee T-Coffee 2016-12-13 http://www.tcoffee.org/ 13.45.0.4846264 t-coffee 13.46.0.919e8c6b To update Sequence Analysis earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 211 229 3783 9125 1 1 1 1 0 0 0 0 212 654 3784 16694
-tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. 2019-04-15 1.1.0 perl-bioperl 1.7.8 To update Text Manipulation nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-treebest_best treebest_best TreeBeST best 2015-08-06 http://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest treebest TreeBeST 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 52 1003 1022 0 0 0 0 0 0 0 0 48 148 1003 3028
-unzip unzip Unzip file 2019-08-01 https://github.com/bmcv 6.0 unzip To update Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1345 1356 6942 7024 1 1 1 1 266 266 2461 2461 1612 4847 9404 28294
+tree_relabeler tree_relabel Relabels the tips of a newick formatted tree. 2019-04-15 1.1.0 perl-bioperl 1.7.8 To update Text Manipulation nml https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+treebest_best treebest_best TreeBeST best 2015-08-06 http://treesoft.sourceforge.net/treebest.shtml 1.9.2.post0 treebest 1.9.2.post1 To update Phylogenetics Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences) Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics earlhaminst https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest treebest TreeBeST 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 52 1003 1022 0 0 0 0 0 0 0 0 48 148 1003 3028
+unzip unzip Unzip file 2019-08-01 https://github.com/bmcv 6.0 unzip To update Convert Formats imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1345 1356 6942 7024 1 1 1 1 266 266 2461 2461 1612 4847 9404 28294
visceral_evaluatesegmentation ip_visceral_evaluatesegmentation Visceral Project - Evaluate Segmentation Tool 2024-09-30 https://github.com/bmcv 0.5-2 visceral-evaluatesegmentation 2015.07.03 To update Imaging imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation evaluatesegmentation-tool 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 20 25 0 0 0 0 0 0 0 0 1 3 20 65
voronoi_tesselation voronoi_tessellation Compute Voronoi tesselation 2024-03-09 https://github.com/bmcv 0.22.0 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 43 43 0 0 0 0 0 0 0 0 3 9 43 129
w4mclassfilter w4mclassfilter Filter W4M data by values or metadata 2018-08-06 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper 0.98.19 r-base To update Metabolomics eschen42 https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 10 2370 2836 0 0 0 0 4 4 1482 1509 13 40 3852 12049
@@ -200,86 +200,85 @@ xcms abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retco
10x_bamtofastq 10x_bamtofastq Converts 10x Genomics BAM to FASTQ 2022-05-10 https://github.com/10XGenomics/bamtofastq 1.4.1 10x_bamtofastq 1.4.1 Up-to-date Convert Formats, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 80 80 307 307 3 3 8 8 1 1 3 3 84 252 318 954
Wound healing scratch assay image analysis woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays 2024-02-29 https://git.embl.de/grp-cba/wound-healing-htm-screen 1.6.1 fiji-morpholibj 1.6.1 Up-to-date Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 31 31 0 0 0 0 0 0 0 0 1 3 31 93
add_line_to_file add_line_to_file Adds a text line to the beginning or end of a file. 2020-11-01 0.1.0 coreutils 8.25 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 378 378 15933 15933 214 214 1736 1736 28 28 380 380 620 1860 18049 54147
-add_value addValue Add a value as a new column. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 1293 1610 37860 374587 1243 6197 17588 293713 202 229 3873 4397 2738 13512 59321 791339
+add_value addValue Add a value as a new column. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1293 1610 37860 374587 1243 6197 17588 293713 202 229 3873 4397 2738 13512 59321 791339
agat agat GTF/GFF analysis toolkit 2023-05-22 https://github.com/NBISweden/AGAT 1.4.0 agat 1.4.2 To update Convert Formats, Statistics, Fasta Manipulation Data handling, Genome annotation Data handling, Genome annotation Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/agat https://github.com/bgruening/galaxytools/tree/master/tools/agat agat AGAT Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 244 244 1436 1436 0 0 0 0 10 10 119 119 254 762 1555 4665
align_back_trans align_back_trans Thread nucleotides onto a protein alignment (back-translation) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0.0.10 biopython 1.70 To update Fasta Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 35 511 541 0 0 0 0 0 0 0 0 32 99 511 1563
antarna antarna antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research . 2015-04-30 1.1 antarna 2.0.1.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 7 292 306 0 0 0 0 0 0 0 0 5 17 292 890
-antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 2015-02-28 https://antismash.secondarymetabolites.org 6.1.1 antismash 7.1.0 To update Sequence Analysis Sequence clustering, Gene prediction, Differential gene expression analysis Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Molecular interactions, pathways and networks, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash antismash antiSMASH 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. 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 726 811 15949 16490 649 649 5113 5113 169 169 6043 6043 1544 4717 27105 81856
+antismash antismash Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 2015-02-28 https://antismash.secondarymetabolites.org 6.1.1 antismash 7.1.0 To update Sequence Analysis Sequence clustering, Gene prediction, Differential gene expression analysis Sequence clustering, Gene prediction, Differential gene expression analysis Molecular interactions, pathways and networks, Gene and protein families Molecular interactions, pathways and networks, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash https://github.com/bgruening/galaxytools/tree/master/tools/antismash antismash antiSMASH 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 726 811 15949 16490 649 649 5113 5113 169 169 6043 6043 1544 4717 27105 81856
aresite2 AREsite2_REST AREsite2 REST Interface 2017-02-01 http://rna.tbi.univie.ac.at/AREsite 0.1.2 python To update RNA, Data Source, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 10 12 59 74 0 0 0 0 0 0 0 0 10 32 59 192
atactk_trim_adapters atactk_trim_adapters Trim adapters from paired-end HTS reads. 2018-06-20 https://github.com/ParkerLab/atactk/ 0.1.6 atactk 0.1.9 To update Fastq Manipulation rnateam https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 62 72 232 279 0 0 0 0 0 0 0 0 62 196 232 743
-augustus augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2015-02-28 http://bioinf.uni-greifswald.de/augustus/ 3.1.0 augustus 3.5.0 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/augustus https://github.com/bgruening/galaxytools/tree/master/tools/augustus 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1378 1509 10109 11052 2206 2206 12573 12573 369 369 5274 5274 3953 11990 27956 84811
bamhash bamhash Hash BAM and FASTQ files to verify data integrity 2015-09-17 https://github.com/DecodeGenetics/BamHash 1.1 bamhash 1.1 Up-to-date Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bamhash https://github.com/bgruening/galaxytools/tree/master/tools/bamhash 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 40 44 158 181 0 0 0 0 0 0 0 0 40 124 158 497
barcode_collapse barcode_collapse Paired End randomer aware duplicate removal algorithm 2016-06-11 https://github.com/YeoLab/gscripts 0.1.0 pysam 0.22.1 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-basecoverage gops_basecoverage_1 Base Coverage of all intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 27 35 226 308 302 2284 2615 45557 32 36 482 522 361 3077 3323 53033
+basecoverage gops_basecoverage_1 Base Coverage of all intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 27 35 226 308 302 2284 2615 45557 32 36 482 522 361 3077 3323 53033
best_regression_subsets BestSubsetsRegression1 Perform Best-subsets Regression 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 3 4 7 72 14 253 0 0 0 0 10 96 17 291
bg_statistical_hypothesis_testing bg_statistical_hypothesis_testing Tool for computing statistical tests. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0.3 numpy To update Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/statistics https://github.com/bgruening/galaxytools/tree/master/tools/statistics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 61 169 346 0 0 0 0 0 0 0 0 46 153 169 684
bia_download bia_download Tool to query ftp links for study from bioimage archive 2023-12-06 0.1.0 wget To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 0 0 0 0 0 0 0 0 2 6 3 9
-bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format 2015-06-04 0.1.0 ucsc_tools To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 567 650 5769 6802 0 0 0 0 0 1 0 3 567 1785 5769 18343
+bigwig_to_bedgraph bigwig_to_bedgraph Convert from bigWig to bedGraph format 2015-06-04 0.1.0 ucsc_tools To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 567 650 5769 6802 0 0 0 0 0 1 0 3 567 1785 5769 18343
bioimage_inference bioimage_inference Load model from BioImage.IO and make inferences 2024-08-02 https://github.com/bgruening/galaxytools 2.4.1 python To update Imaging Machine learning, Computer science Machine learning bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging pytorch PyTorch PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. pytorch 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 2 2 0 0 0 0 0 0 0 0 1 3 2 6
biomodels biomodels_biomd0000001066, biomodels_biomd0000001076 Wrappers for tools to bring BioModels AI models into Galaxy. 2023-11-07 https://www.ebi.ac.uk/biomodels/ 1.1 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 25 25 0 0 0 0 0 0 0 0 11 33 25 75
bionano bionano_scaffold Bionano Solve is a set of tools for analyzing Bionano data 2021-05-17 https://bionanogenomics.com/ 3.7.0 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bionano https://github.com/bgruening/galaxytools/tree/master/tools/bionano 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 151 151 547 547 43 43 143 143 22 22 596 596 216 648 1286 3858
-bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states 2015-02-28 https://www.bioinformatics.babraham.ac.uk/projects/bismark/ 0.22.1 bismark 0.24.2 To update Sequence Analysis, Next Gen Mappers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0 4 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 992 1099 13715 14997 0 0 0 0 22 22 197 197 1014 3149 13912 43018
+bismark bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor A tool to map bisulfite converted sequence reads and determine cytosine methylation states 2015-02-28 https://www.bioinformatics.babraham.ac.uk/projects/bismark/ 0.22.1 bismark 0.24.2 To update Sequence Analysis, Next Gen Mappers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/bismark https://github.com/bgruening/galaxytools/tree/master/tools/bismark 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 992 1099 13715 14997 0 0 0 0 22 22 197 197 1014 3149 13912 43018
black_forest_labs_flux black_forest_labs_flux Using the black forest labs FLUX.1 models to generate image based on user input. 2024-10-14 https://github.com/bgruening/galaxytools/tree/master/tools/flux 2024 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flux https://github.com/bgruening/galaxytools/tree/master/tools/flux 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blat_coverage_report generate_coverage_report Polymorphism of the Reads 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blat_mapping blat2wig Coverage of the Reads in wiggle format 2014-05-19 1.0.0 To update Next Gen Mappers, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
blobtoolkit blobtoolkit Identification and isolation non-target data in draft and publicly available genome assemblies. 2022-11-04 https://blobtoolkit.genomehubs.org/ 4.0.7 To update Sequence Analysis, Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 79 79 1527 1527 1 1 6 6 26 26 317 317 106 318 1850 5550
blockbuster blockbuster Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach. 2015-02-28 http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html 0.1.2 blockbuster 0.0.1.1 To update RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 97 119 768 3043 11 11 14 14 9 9 276 276 117 373 1058 5449
blockclust blockclust BlockClust detects transcripts with similar processing patterns. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust 1.1.1 blockclust 1.1.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 54 79 811 1501 29 29 64 64 15 15 561 561 98 319 1436 4998
-bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. 2012-11-26 http://bowtie-bio.sourceforge.net/ 1.2.0 bowtie 1.3.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1320 1480 24164 25149 1330 17491 17537 203397 291 351 15654 15992 2941 25204 57355 359248
+bowtie_wrappers bowtie_wrapper Galaxy wrappers for the Bowtie short read mapping tools. 2012-11-26 http://bowtie-bio.sourceforge.net/ 1.2.0 bowtie 1.3.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1320 1480 24164 25149 1330 17491 17537 203397 291 351 15654 15992 2941 25204 57355 359248
canonical_correlation_analysis cca1 Canonical Correlation Analysis 2014-05-19 1.0.0 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 18 66 75 31 147 141 505 0 0 0 0 47 259 207 994
-canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu 2.2 canu 2.2 Up-to-date De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1383 1444 13360 14618 0 0 0 0 385 385 3542 3542 1768 5365 16902 51964
+canu canu Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). 2018-06-07 https://github.com/marbl/canu 2.2 canu 2.2 Up-to-date De-novo assembly De-novo assembly Genomics Genomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/canu https://github.com/bgruening/galaxytools/tree/master/tools/canu canu CANU De-novo assembly tool for long read chemistry like Nanopore data and PacBio data. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1383 1444 13360 14618 0 0 0 0 385 385 3542 3542 1768 5365 16902 51964
categorize_elements_satisfying_criteria categorize_elements_satisfying_criteria Categorize Elements satisfying criteria. 2013-09-25 1.0.0 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 5 37 41 0 0 0 0 12 14 168 186 16 51 205 637
ccat peakcalling_ccat Control-based ChIP-seq Analysis Tool 2014-01-27 0.0.2 ccat 3.0 To update ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 39 88 175 0 0 0 0 0 0 0 0 28 95 88 351
-cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 407 628 5946 7379 0 0 0 0 407 1442 5946 19271
+cd_hit_dup cd_hit_dup simple tool for removing duplicates from sequencing reads 2015-04-28 0.0.1 cd-hit-auxtools 4.8.1 To update Metagenomics, Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 407 628 5946 7379 0 0 0 0 407 1442 5946 19271
cellpose cellpose Cellpose is an anatomical segmentation algorithm 2024-02-29 https://github.com/MouseLand/cellpose 3.0.10 cellpose To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cellpose https://github.com/bgruening/galaxytools/tree/master/tools/cellpose 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 14 14 0 0 0 0 0 0 0 0 4 12 14 42
cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper 2020-03-06 To update Imaging Quantification, Image analysis, Parsing Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype Imaging, Microarray experiment, Genotype and phenotype bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler CellProfiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. cellprofiler 0 23 23 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 23 19 0 749 749 4773 4773 0 0 0 0 94 94 5688 5688 843 2529 10461 31383
-cellprofiler4 cp_cellprofiler4 cellProfiler4 wrapper 2021-09-15 https://github.com/CellProfiler/CellProfiler 4.2.8 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 55 55 0 0 0 0 0 0 0 0 11 33 55 165
-change_case ChangeCase Convert column case. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 2204 2547 10606 12531 1748 2394 9044 17167 240 245 923 938 4192 13570 20573 71782
+cellprofiler4 cp_cellprofiler4 cellProfiler4 wrapper 2021-09-15 https://github.com/CellProfiler/CellProfiler 4.2.8 To update Imaging bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 55 55 0 0 0 0 0 0 0 0 11 33 55 165
+change_case ChangeCase Convert column case. 2012-12-04 1.0.1 perl To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 2204 2547 10606 12531 1748 2394 9044 17167 240 245 923 938 4192 13570 20573 71782
chatgpt_openai_api chatgpt_openai_api Using the OpenAI GPT models to generate text based on user input. 2024-08-12 https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 2024 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 62 62 0 0 0 0 0 0 0 0 12 36 62 186
chipseeker chipseeker A tool for ChIP peak annotation and visualization 2018-05-24 https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html 1.32.0 bioconductor-chipseeker 1.38.0 To update ChIP-seq, Genome annotation rnateam https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 956 991 16468 18344 2559 2625 33692 34453 104 104 2948 2948 3619 10958 53108 161961
chromosome_diagram chromosome_diagram Chromosome Diagrams using Biopython 2013-09-26 0.0.3 biopython 1.70 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
circexplorer circexplorer A combined strategy to identify circular RNAs (circRNAs and ciRNAs) 2016-06-06 https://github.com/YangLab/CIRCexplorer 1.1.9.0 circexplorer 1.1.10 To update Sequence Analysis, RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 40 211 263 0 0 0 0 6 6 209 209 38 122 420 1312
clc_assembly_cell clc_assembler, clc_mapper Galaxy wrapper for the CLC Assembly Cell suite from CLCBio 2013-10-28 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0.0.7 samtools 1.21 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
clinod clinod NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins 2013-05-02 http://www.compbio.dundee.ac.uk/www-nod/ 0.1.0 clinod 1.3 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod clinod clinod 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. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 548 548 0 0 0 0 18 54 548 1644
-cluster gops_cluster_1 Cluster the intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18 35 513 813 156 1547 2406 30579 17 20 1353 1393 191 1984 4272 41329
+cluster gops_cluster_1 Cluster the intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 18 35 513 813 156 1547 2406 30579 17 20 1353 1393 191 1984 4272 41329
cmsearch_deoverlap cmsearch_deoverlap removes lower scoring overlaps from cmsearch results. 2023-08-19 https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl 0.08+galaxy2 perl To update RNA Comparison, Alignment Comparison, Alignment Biology, Medicine Biology, Medicine rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap cmsearch-deoverlap cmsearch-deoverlap Removes lower scoring overlaps from cmsearch results.This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 3 3 2609 2609 0 0 0 0 0 0 0 0 3 9 2609 7827
cmv cmcv, cmv, hmmcv, hmmv cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models. 2017-09-22 https://github.com/eggzilla/cmv 1.0.8 cmv 1.0.8 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 11 14 90 112 0 0 0 0 0 0 0 0 11 36 90 292
cofold cofold Cofold predicts RNA secondary structures that takes co-transcriptional folding into account. 2015-02-28 http://www.e-rna.org/cofold/ 2.0.4.0 cofold 2.0.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25 29 316 355 0 0 0 0 0 0 0 0 25 79 316 987
-column_arrange_by_header bg_column_arrange_by_header Column arrange by header name 2015-03-02 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 446 484 5356 5636 375 375 2026 2026 117 138 1400 1531 938 2873 8782 26757
+column_arrange_by_header bg_column_arrange_by_header Column arrange by header name 2015-03-02 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 446 484 5356 5636 375 375 2026 2026 117 138 1400 1531 938 2873 8782 26757
combine_metaphlan2_humann2 combine_metaphlan_humann Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 2023-07-20 0.3.0 python To update Metagenomics Aggregation Aggregation Metagenomics, Molecular interactions, pathways and networks Metagenomics, Molecular interactions, pathways and networks bebatut https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann combine_metaphlan_and_humann Combine Metaphlan and HUMAnN This tool combine MetaPhlAn outputs and HUMANnN outputs 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 65 65 530 530 6 6 8 8 0 0 0 0 71 213 538 1614
compalignp compalignp Compute fractional identity between trusted alignment and test alignment 2015-06-03 1.0 compalignp 1.0 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 28 39 221 0 0 0 0 0 0 0 0 5 38 39 299
compare_humann2_output compare_humann2_output Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2022-10-19 0.2.0 To update Metagenomics Comparison Comparison Metagenomics, Gene and protein families Metagenomics, Gene and protein families bebatut https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output compare_humann2_outputs Compare HUMAnN2 outputs This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 28 32 306 332 0 0 0 0 0 0 0 0 28 88 306 944
-complement gops_complement_1 Complement intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15 20 187 233 165 836 495 4810 7 7 405 451 187 1237 1087 7668
+complement gops_complement_1 Complement intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 15 20 187 233 165 836 495 4810 7 7 405 451 187 1237 1087 7668
compute_motif_frequencies_for_all_motifs compute_motif_frequencies_for_all_motifs Compute Motif Frequencies For All Motifs, motif by motif. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 10 85 96 0 0 0 0 8 8 316 334 17 52 401 1232
compute_motifs_frequency compute_motifs_frequency Compute Motif Frequencies in indel flanking regions. 2013-09-25 1.0.0 To update Sequence Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 2 55 65 0 0 0 0 5 5 317 335 7 21 372 1144
compute_q_values compute_q_values Compute q-values based on multiple simultaneous tests p-values 2014-04-01 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 35 0 0 0 0 0 0 0 0 0 3 0 35
-concat gops_concat_1 Concatenate two bed files 2014-04-01 https://github.com/galaxyproject/gops 1.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 694 783 575128 575441 629 3508 43420 85345 104 117 19330 19418 1427 7262 637878 1955960
-condense_characters Condense characters1 Condense consecutive characters. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 368 47 2173 8 8 195 205 36 448 242 2862
-convert_characters Convert characters1 Convert delimiters to tab. 2012-12-04 1.0.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 1061 1200 23589 28986 2302 8699 23507 160693 251 329 5413 6446 3614 17456 52509 301143
+concat gops_concat_1 Concatenate two bed files 2014-04-01 https://github.com/galaxyproject/gops 1.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 694 783 575128 575441 629 3508 43420 85345 104 117 19330 19418 1427 7262 637878 1955960
+condense_characters Condense characters1 Condense consecutive characters. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 368 47 2173 8 8 195 205 36 448 242 2862
+convert_characters Convert characters1 Convert delimiters to tab. 2012-12-04 1.0.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1061 1200 23589 28986 2302 8699 23507 160693 251 329 5413 6446 3614 17456 52509 301143
convert_solid_color2nuc color2nuc Convert Color Space to Nucleotides 2014-05-19 1.0.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
coprarna coprarna Target prediction for prokaryotic trans-acting small RNAs 2017-11-01 https://github.com/PatrickRWright/CopraRNA 2.1.1 coprarna 2.1.4 To update RNA, Sequence Analysis rnateam https://github.com/PatrickRWright/CopraRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
correlation cor2 Correlation for numeric columns 2014-07-28 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 106 134 398 876 105 755 412 5568 21 27 192 239 232 1380 1002 8687
count_gff_features count_gff_features Count GFF Features 2014-07-28 0.2 galaxy-ops 1.1.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 110 124 280 307 332 628 712 1277 55 79 476 541 497 1825 1468 5061
-count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file 2016-02-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 43 58 1560 1725 193 2113 4328 44209 16 18 283 316 252 2693 6171 58592
-coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth 2014-11-20 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+count_roi_variants count_roi_variants Count sequence variants in region of interest in BAM file 2016-02-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0.0.6 samtools 1.21 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+coverage gops_coverage_1 Coverage of a set of intervals on second set of intervals 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 43 58 1560 1725 193 2113 4328 44209 16 18 283 316 252 2693 6171 58592
+coverage_stats coverage_stats BAM coverage statistics using samtools idxstats and depth 2014-11-20 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0.1.0 samtools 1.21 To update Assembly, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cpat cpat Coding-potential assessment tool using an alignment-free logistic regression model. 2023-02-01 https://github.com/liguowang/cpat 3.0.5 cpat 3.0.5 Up-to-date Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/cpat https://github.com/bgruening/galaxytools/tree/master/tools/cpat 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 47 47 204 204 40 40 165 165 7 7 125 125 94 282 494 1482
create_tool_recommendation_model create_tool_recommendation_model Create model to recommend tools 2019-08-20 https://github.com/bgruening/galaxytools 0.0.5 python To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 25 445 445 32 32 71 71 0 0 0 0 57 171 516 1548
-crispr_recognition_tool crispr_recognition_tool CRISPR Recognition Tool 2015-02-28 1.2.0 crisper_recognition_tool 1.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 180 4066 4139 0 0 0 0 0 0 0 0 166 512 4066 12271
+crispr_recognition_tool crispr_recognition_tool CRISPR Recognition Tool 2015-02-28 1.2.0 crisper_recognition_tool 1.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/crt https://github.com/bgruening/galaxytools/tree/master/tools/crt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 166 180 4066 4139 0 0 0 0 0 0 0 0 166 512 4066 12271
ctd_batch ctdBatch_1 CTD analysis of chemicals, diseases, or genes 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 41 48 196 211 1 161 1 447 0 0 0 0 42 293 197 1052
cummerbund cummeRbund Wrapper for the Bioconductor cummeRbund library 2015-04-24 https://bioconductor.org/packages/release/bioc/html/cummeRbund.html 2.16.0 fonts-conda-ecosystem To update RNA, Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 98 166 1251 1803 486 2044 3461 15159 57 159 2425 3338 641 3651 7137 34574
cummerbund_to_tabular cummerbund_to_cuffdiff Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. 2014-12-22 1.0.1 To update Convert Formats, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43 97 888 1208 101 479 1334 2683 0 0 0 0 144 864 2222 8335
-cut_columns Cut1 Select columns from a dataset. 2012-12-04 1.0.2 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 11939 12833 1973168 2034965 12967 30199 352364 803522 2341 2572 128777 133584 27247 100098 2454309 7880689
+cut_columns Cut1 Select columns from a dataset. 2012-12-04 1.0.2 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 11939 12833 1973168 2034965 12967 30199 352364 803522 2341 2572 128777 133584 27247 100098 2454309 7880689
delete_overlapping_indels delete_overlapping_indels Delete Overlapping Indels from a chromosome indels file 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 7 33 40 0 0 0 0 0 0 0 0 6 19 33 106
dewseq dewseq DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data 2022-10-20 https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers 0.1.0+galaxy0 python To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 18 18 89 89 0 0 0 0 0 0 0 0 18 54 89 267
dgidb_annotator dgidb_annotate Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/) 2013-11-28 0.1 To update Systems Biology, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 30 59 69 0 133 0 304 0 0 0 0 26 215 59 491
-diff diff GNU diff tool that calculates the differences between two files. 2020-03-29 http://www.gnu.org/software/diffutils/ 3.7 diffutils To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 99 99 362 362 17 17 23 23 0 0 0 0 116 348 385 1155
+diff diff GNU diff tool that calculates the differences between two files. 2020-03-29 http://www.gnu.org/software/diffutils/ 3.10 diffutils To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diff https://github.com/bgruening/galaxytools/tree/master/tools/diff 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 99 99 362 362 17 17 23 23 0 0 0 0 116 348 385 1155
diffbind Diffbind provides functions for processing ChIP-Seq data. 2015-02-28 http://bioconductor.org/packages/release/bioc/html/DiffBind.html To update ChIP-seq bgruening https://github.com/bgruening/galaxytools/tree/master/tools/diffbind https://github.com/bgruening/galaxytools/tree/master/tools/diffbind 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
divide_pg_snp dividePgSnp Separate pgSnp alleles into columns 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 9 26 32 20 53 86 172 0 0 0 0 28 118 112 428
dorina dorina_search data source for RNA interactions in post-transcriptional regulation 2015-05-20 1.0 To update RNA, Data Source rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 31 921 1626 0 0 0 0 0 0 0 0 4 39 921 3468
dot2ct rnastructure_dot2ct Dot-Bracket to Connect Table (CT) 2015-06-10 5.7.a rnastructure 6.4 To update Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dotknot dotknot DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence 2015-09-17 http://dotknot.csse.uwa.edu.au/ 1.3.1 vienna_rna To update RNA, Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 12 15 74 88 0 0 0 0 0 0 0 0 12 39 74 236
-draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria 2013-09-25 1.0.0 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 52 189 216 0 0 0 0 22 31 183 213 69 221 372 1173
+draw_stacked_barplots draw_stacked_barplots Draw Stacked Bar Plots for different categories and different criteria 2013-09-25 1.0.0 R To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 47 52 189 216 0 0 0 0 22 31 183 213 69 221 372 1173
dwt_cor_ava_perclass compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 11 136 141 8 27 136 413
dwt_cor_avb_all compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 124 124 7 21 124 372
dwt_ivc_all compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom Compute P-values and Second Moments for Feature Occurrences 2014-01-27 1.0.1 r-waveslim 1.7.5 To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 7 121 123 5 17 121 365
@@ -290,35 +289,35 @@ effectivet3 effectiveT3 Find bacterial type III effectors in protein sequences 2
epicseg epicseg_segment EpiCSeg is a tool for conducting chromatin segmentation. 2018-03-02 https://github.com/lamortenera/epicseg @VERSION_STRING@ epicseg 1.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/epicseg https://github.com/bgruening/galaxytools/tree/master/tools/epicseg 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 21 160 252 0 0 0 0 0 0 0 0 17 55 160 572
erga_ear make_ear A tool to compile assembly reports and stastics from assembly pipeline 2024-06-07 https://github.com/ERGA-consortium/EARs/tree/main 24.10.15 reportlab To update Sequence Analysis, Assembly bgruening https://github.com/ERGA-consortium/EARs/tree/main https://github.com/bgruening/galaxytools/tree/master/tools/ear 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 28 28 0 0 0 0 0 0 0 0 2 6 28 84
exparna exparna ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. 2015-02-28 http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp 1.0.1 exparna 1.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-express express Quantify the abundances of a set of target sequences from sampled subsequences 2014-01-27 1.1.1 eXpress 1.5.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 45 278 337 0 117 0 1184 23 60 2402 2844 57 336 2680 9725
-fasta_compute_length fasta_compute_length Compute sequence length 2014-05-19 https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.4 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 978 1129 8547 9136 1404 5670 17748 51150 162 190 4239 4404 2544 12077 30534 125758
-fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species 2014-05-19 0.0.1 bx-python 0.13.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 242 255 39695 39742 600 1398 13660 19007 92 112 1521 1603 934 3633 54876 170104
+express express Quantify the abundances of a set of target sequences from sampled subsequences 2014-01-27 1.1.1 eXpress 1.5.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/express https://github.com/galaxyproject/tools-devteam/tree/main/tools/express 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 45 278 337 0 117 0 1184 23 60 2402 2844 57 336 2680 9725
+fasta_compute_length fasta_compute_length Compute sequence length 2014-05-19 https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length 1.0.4 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 978 1129 8547 9136 1404 5670 17748 51150 162 190 4239 4404 2544 12077 30534 125758
+fasta_concatenate_by_species fasta_concatenate0 Concatenate FASTA alignment by species 2014-05-19 0.0.1 bx-python 0.13.0 To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 242 255 39695 39742 600 1398 13660 19007 92 112 1521 1603 934 3633 54876 170104
fasta_filter_by_id fasta_filter_by_id Filter FASTA sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fasta_filter_by_length fasta_filter_by_length Filter sequences by length 2014-05-19 1.2 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 889 997 47494 51924 1488 3742 50663 101663 241 276 3919 5601 2618 10251 102076 363340
-fasta_to_tabular fasta2tab FASTA-to-Tabular converter 2014-05-19 1.1.1 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1572 1793 108876 113638 2209 8565 82527 192112 275 334 5711 7649 4056 18804 197114 707627
+fasta_filter_by_length fasta_filter_by_length Filter sequences by length 2014-05-19 1.2 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 889 997 47494 51924 1488 3742 50663 101663 241 276 3919 5601 2618 10251 102076 363340
+fasta_to_tabular fasta2tab FASTA-to-Tabular converter 2014-05-19 1.1.1 python To update Fasta Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1572 1793 108876 113638 2209 8565 82527 192112 275 334 5711 7649 4056 18804 197114 707627
fastq_filter_by_id fastq_filter_by_id Filter FASTQ sequences by ID (DEPRECATED) 2017-02-02 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0.0.7 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fastq_info fastq_info FASTQ info allows to validate single or paired fastq files 2021-09-12 https://github.com/nunofonseca/fastq_utils 0.25.1 fastq_utils 0.25.2 To update Fastq Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1266 1266 7560 7560 1581 1581 6539 6539 0 0 0 0 2847 8541 14099 42297
+fastq_info fastq_info FASTQ info allows to validate single or paired fastq files 2021-09-12 https://github.com/nunofonseca/fastq_utils 0.25.1 fastq_utils 0.25.2 To update Fastq Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1266 1266 7560 7560 1581 1581 6539 6539 0 0 0 0 2847 8541 14099 42297
fastq_pair_names fastq_pair_names Extract FASTQ paired read names 2014-05-05 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0.0.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_paired_unpaired fastq_paired_unpaired Divide FASTQ file into paired and unpaired reads 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0.1.5 galaxy_sequence_utils 1.2.0 To update Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_trimmer_by_quality fastq_quality_trimmer FASTQ Quality Trimmer by sliding window 2014-01-27 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 859 967 4881 6165 3455 11369 29458 99179 259 338 2171 2678 4573 21820 36510 181042
fastqsolexa_to_fasta_qual fastqsolexa_to_fasta_qual FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 2014-05-19 1.0.0 To update Convert Formats, Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 8 0 0 0 0 0 3 0 8
-featurecounter featureCoverage1 Feature coverage 2014-04-01 2.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 19 22308 22388 54 349 350 13711 0 0 0 0 70 508 22658 81415
+featurecounter featureCoverage1 Feature coverage 2014-04-01 2.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 19 22308 22388 54 349 350 13711 0 0 0 0 70 508 22658 81415
filter_transcripts_via_tracking filter_combined_via_tracking Filter Combined Transcripts 2014-01-27 0.1 To update RNA devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 10 23 24 26 241 62 635 2 2 2 2 37 327 87 835
-find_diag_hits find_diag_hits Find diagnostic hits 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 12 62 70 1 204 3 1787 0 0 0 0 11 238 65 1987
+find_diag_hits find_diag_hits Find diagnostic hits 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 12 62 70 1 204 3 1787 0 0 0 0 11 238 65 1987
find_subsequences bg_find_subsequences 2015-03-19 0.3 biopython 1.70 To update bgruening https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 69 79 554 784 323 361 2820 3047 1 1 20 20 393 1227 3394 10639
-flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval 2014-04-01 https://github.com/galaxyproject/gops 4.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 51 63 589 731 304 2549 2445 32847 15 22 1214 1294 370 3374 4248 43368
+flanking_features flanking_features_1 Fetch closest non-overlapping feature for every interval 2014-04-01 https://github.com/galaxyproject/gops 4.0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 51 63 589 731 304 2549 2445 32847 15 22 1214 1294 370 3374 4248 43368
flexynesis flexynesis This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction. 2024-08-12 https://github.com/BIMSBbioinfo/flexynesis/tree/main 0.2.10 flexynesis 0.2.10 Up-to-date Machine Learning, Statistics, Systems Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 9 9 0 0 0 0 0 0 0 0 2 6 9 27
-flye flye Assembly of long and error-prone reads. 2018-09-22 https://github.com/fenderglass/Flye/ 2.9.5 flye 2.9.5 Up-to-date Assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Sequence assembly, Metagenomics, Whole genome sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye Flye Flye 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3379 3422 32514 32675 2537 2537 19434 19434 1624 1624 9843 9843 7540 22663 61791 185534
+flye flye Assembly of long and error-prone reads. 2018-09-22 https://github.com/fenderglass/Flye/ 2.9.5 flye 2.9.5 Up-to-date Assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly Sequence assembly, Metagenomics, Whole genome sequencing, Genomics Sequence assembly, Metagenomics, Whole genome sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/flye https://github.com/bgruening/galaxytools/tree/master/tools/flye Flye Flye 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3379 3422 32514 32675 2537 2537 19434 19434 1624 1624 9843 9843 7540 22663 61791 185534
footprint footprint Find transcription factor footprints 2017-04-18 https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/ 1.0.0 footprint 1.0.1 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/footprint https://github.com/bgruening/galaxytools/tree/master/tools/footprint 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 57 57 0 0 0 0 0 0 0 0 5 15 57 171
format_cd_hit_output format_cd_hit_output Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 2022-10-19 1.0.0+galaxy1 To update Fasta Manipulation bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 60 189 203 0 0 0 0 0 0 0 0 57 174 189 581
-format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2022-10-19 0.2.0 To update Metagenomics Formatting Formatting Taxonomy, Metagenomics Taxonomy, Metagenomics bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 558 608 5940 6474 0 0 0 0 0 0 0 0 558 1724 5940 18354
+format_metaphlan2_output format_metaphlan2_output Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2022-10-19 0.2.0 To update Metagenomics Formatting Formatting Taxonomy, Metagenomics Taxonomy, Metagenomics bebatut https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/ https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output format_metaphlan2_output Format metaphlan2 output This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 558 608 5940 6474 0 0 0 0 0 0 0 0 558 1724 5940 18354
generate_pc_lda_matrix generate_matrix_for_pca_and_lda1 Generate a Matrix for using PC and LDA 2014-07-28 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 29 30 115 124 102 261 518 1029 14 17 184 198 145 598 817 2985
-get_flanks get_flanks1 Get flanks returns flanking region/s for every gene 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1462 2044 3768 325011 2201 6583 9350 242043 119 146 787 1070 3782 16337 13905 595934
-get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 136 136 746 746 0 0 0 0 244 244 1504 1504 380 1140 2250 6750
+get_flanks get_flanks1 Get flanks returns flanking region/s for every gene 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1462 2044 3768 325011 2201 6583 9350 242043 119 146 787 1070 3782 16337 13905 595934
+get_orfs_or_cdss get_orfs_or_cdss Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs) 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0.2.3 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 136 136 746 746 0 0 0 0 244 244 1504 1504 380 1140 2250 6750
getindelrates_3way indelRates_3way Estimate Indel Rates for 3-way alignments 2014-04-01 1.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 86 70 290 0 0 0 0 20 126 70 430
getindels_2way getIndels_2way Fetch Indels from pairwise alignments 2014-04-01 1.0.0 numpy To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 61 74 237 0 0 0 0 24 109 74 385
-gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. 2022-03-08 https://github.com/vgl-hub/gfastats 1.3.9 gfastats 1.3.9 Up-to-date Sequence Analysis Data handling Data handling Computational biology Computational biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 767 767 11748 11748 397 397 6560 6560 106 106 2556 2556 1270 3810 20864 62592
-gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.1.1 taxonomy 0.10.0 To update Metagenomics Database search, ID mapping Database search, ID mapping Taxonomy Taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy gi2taxonomy gi2taxonomy 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). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 74 109 490 682 20 1798 127 14058 0 0 0 0 94 2095 617 15974
+gfastats gfastats Tool for generating sequence statistics and simultaneous genome assembly file manipulation. 2022-03-08 https://github.com/vgl-hub/gfastats 1.3.9 gfastats 1.3.9 Up-to-date Sequence Analysis Data handling Data handling Computational biology Computational biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/gfastats https://github.com/bgruening/galaxytools/tree/master/tools/gfastats gfastats gfastats gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 767 767 11748 11748 397 397 6560 6560 106 106 2556 2556 1270 3810 20864 62592
+gi2taxonomy Fetch Taxonomic Ranks Fetch taxonomic representation 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.1.1 taxonomy 0.10.0 To update Metagenomics Database search, ID mapping Database search, ID mapping Taxonomy Taxonomy devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy gi2taxonomy gi2taxonomy 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). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 74 109 490 682 20 1798 127 14058 0 0 0 0 94 2095 617 15974
glimmer_hmm GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM) 2015-02-28 https://ccb.jhu.edu/software/glimmerhmm/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gmaj gmaj_1 GMAJ Multiple Alignment Viewer 2014-01-27 2.0.1 To update Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 6 11 11 29 230 85 984 7 8 10 11 42 328 106 1218
gotohscan rbc_gotohscan Find subsequences in db 2015-07-02 1.3.0 gotohscan 1.3 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 7 34 72 0 0 0 0 0 0 0 0 5 17 34 140
@@ -336,14 +335,14 @@ graphclust_postprocessing_no_align graphclust_glob_report_no_align Redundant Gra
graphclust_prepocessing_for_mlocarna preMloc This tool prepares files for locarna step. 2016-12-15 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 48 62 1202 2121 0 0 0 0 0 0 0 0 48 158 1202 4525
graphclust_preprocessing preproc Preprocessing input for GraphClust 2016-12-15 0.5 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 71 1116 1897 0 0 0 0 0 0 0 0 57 185 1116 4129
graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick 2016-12-26 http://www.graphicsmagick.org 1.3.45 graphicsmagick 1.3.26 To update Imaging bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 97 99 1725 2708 2 2 2 2 0 0 0 0 99 299 1727 6164
-graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. 2018-09-27 https://github.com/isovic/graphmap/ 0.5.2 graphmap 0.6.4 To update Assembly Sequence trimming, EST assembly, Read mapping Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing Gene transcripts, RNA-Seq, RNA splicing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 323 338 7012 7344 0 0 0 0 0 0 0 0 323 984 7012 21368
+graphmap graphmap_align, graphmap_overlap Mapper for long, error-prone reads. 2018-09-27 https://github.com/isovic/graphmap/ 0.5.2 graphmap 0.6.4 To update Assembly Sequence trimming, EST assembly, Read mapping Sequence trimming, EST assembly, Read mapping Gene transcripts, RNA-Seq, RNA splicing Gene transcripts, RNA-Seq, RNA splicing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/graphmap https://github.com/bgruening/galaxytools/tree/master/tools/graphmap graphmap graphmap Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 323 338 7012 7344 0 0 0 0 0 0 0 0 323 984 7012 21368
graphprot graphprot_predict_profile GraphProt models binding preferences of RNA-binding proteins. 2018-05-24 https://github.com/dmaticzka/GraphProt 1.1.7+galaxy2 graphprot 1.1.7 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 18 19 463 484 0 0 0 0 0 0 0 0 18 55 463 1410
hclust2 hclust2 Plots heatmaps 2018-07-22 https://bitbucket.org/nsegata/hclust2/ 0.99 hclust2 1.0.0 To update Data Visualization rnateam https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2 https://github.com/bgruening/galaxytools/tree/master/tools/hclust2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hgv_fundo hgv_funDo FunDO human genes associated with disease terms 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 33 397 145 1794 0 0 0 0 33 463 145 2084
hgv_hilbertvis hgv_hilbertvis HVIS visualization of genomic data with the Hilbert curve 2013-09-25 https://www.ebi.ac.uk/huber-srv/hilbert/ 1.0.0 R To update Graphics, Visualization devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 16 60 119 265 0 0 0 0 16 92 119 503
hictk hictk Convert cooler to juicebox_hic 2024-02-03 https://github.com/paulsengroup/hictk 2.0.1 hictk 2.0.1 Up-to-date Convert Formats, Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hictk https://github.com/bgruening/galaxytools/tree/master/tools/hictk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 17 17 0 0 0 0 0 0 0 0 9 27 17 51
hicup hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater The HiCUP-Pipeline from the Bioinformatics Babraham Institute. 2017-03-09 https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html 0.9.2 To update Epigenetics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hicup https://github.com/bgruening/galaxytools/tree/master/tools/hicup 7 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 0 160 184 901 1020 111 111 440 440 0 0 0 0 271 837 1341 4142
-hisat hisat HISAT is a fast and sensitive spliced alignment program. 2015-05-13 http://ccb.jhu.edu/software/hisat/index.shtml 1.0.3 hisat To update Assembly devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 228 0 0 0 0 0 0 0 0 0 12 0 228
+hisat hisat HISAT is a fast and sensitive spliced alignment program. 2015-05-13 http://ccb.jhu.edu/software/hisat/index.shtml 1.0.3 hisat To update Assembly devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 228 0 0 0 0 0 0 0 0 0 12 0 228
histogram histogram_rpy Histogram of a numeric column 2014-07-28 1.0.4 rpy2 2.7.8 To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 866 1002 3748 4661 1507 7101 5993 48272 152 253 549 746 2525 13406 10290 74259
homer Software for motif discovery and next generation sequencing analysis. 2015-02-28 http://homer.salk.edu/homer/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/homer https://github.com/bgruening/galaxytools/tree/master/tools/homer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
htseq_clip htseq_clip htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets 2022-10-11 https://github.com/EMBL-Hentze-group/htseq-clip 0.1.0+galaxy0 htseq-clip 2.19.0b0 To update Sequence Analysis, RNA, CLIP-seq rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 19 19 98 98 0 0 0 0 0 0 0 0 19 57 98 294
@@ -357,13 +356,13 @@ intarna intarna Efficient RNA-RNA interaction prediction incorporating accessibi
intersect gops_intersect_1 Intersect the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2351 3007 20472 349984 4359 14116 45587 778988 484 561 6087 7417 7194 32072 72146 1280681
iprscan5 Interproscan queries the interpro database and provides annotations. 2015-02-28 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
itsx itsx ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences. 2022-05-02 https://microbiology.se/software/itsx/ 1.1.3 itsx 1.1.3 Up-to-date Metagenomics Sequence feature detection Sequence feature detection Functional, regulatory and non-coding RNA, Microbiology Functional, regulatory and non-coding RNA, Microbiology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/itsx https://github.com/bgruening/galaxytools/tree/master/tools/itsx ITSx ITSx 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. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 71 71 1426 1426 0 0 0 0 0 0 0 0 71 213 1426 4278
-jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool 2024-06-04 https://jbrowse.org 2.17.0 jbrowse2 2.17.0 Up-to-date Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 219 219 1312 1312 58 58 116 116 6 6 37 37 283 849 1465 4395
-join gops_join_1 Join the intervals of two datasets side-by-side 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1864 2438 15624 330820 10198 39421 52317 513688 213 289 1329 1645 12275 66698 69270 984693
-join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. 2017-11-26 1.0.1 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 345 410 1980 2697 0 0 0 0 44 44 1081 1081 389 1232 3061 9900
+jbrowse2 jbrowse2 JBrowse2 Genome Browser integrated as a Galaxy Tool 2024-06-04 https://jbrowse.org 2.17.0 jbrowse2 2.18.0 To update Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 219 219 1312 1312 58 58 116 116 6 6 37 37 283 849 1465 4395
+join gops_join_1 Join the intervals of two datasets side-by-side 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1864 2438 15624 330820 10198 39421 52317 513688 213 289 1329 1645 12275 66698 69270 984693
+join_files_on_column_fuzzy join_files_on_column_fuzzy Join two files on a common column, allowing a certain difference. 2017-11-26 1.0.1 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 345 410 1980 2697 0 0 0 0 44 44 1081 1081 389 1232 3061 9900
kernel_canonical_correlation_analysis kcca1 Kernel Canonical Correlation Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 4 62 70 27 71 207 334 0 0 0 0 31 137 269 942
kernel_principal_component_analysis kpca1 Kernel Principal Component Analysis 2014-05-19 1.0.0 rpy To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 30 144 157 83 248 268 707 0 0 0 0 109 496 412 1688
kinwalker Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event. 2015-02-28 http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. 2015-08-05 https://bitbucket.org/natefoo/taxonomy 1.2+galaxy0 gawk To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1060 1061 23008 23014 1719 2168 16194 24490 436 436 14898 14898 3215 10095 54100 170602
+kraken2tax Kraken2Tax Convert Kraken output to Galaxy taxonomy data. 2015-08-05 https://bitbucket.org/natefoo/taxonomy 1.2+galaxy0 gawk To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1060 1061 23008 23014 1719 2168 16194 24490 436 436 14898 14898 3215 10095 54100 170602
labels bg_labels remaps and annotates alignments 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/labels 1.0.5.0 labels To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/labels https://github.com/bgruening/galaxytools/tree/master/tools/labels 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lastz_paired_reads lastz_paired_reads_wrapper Galaxy wrapper for the Lastz alignment tool on paired reads 2012-11-26 1.1.1 lastz 1.04.22 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3 4 7 9 0 0 0 0 5 5 8 10 8 25 15 49
lca_wrapper lca1 Find lowest diagnostic rank 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.1 taxonomy 0.10.0 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4 20 89 137 15 1112 118 6136 0 0 0 0 19 1170 207 6687
@@ -373,16 +372,16 @@ linear_regression LinearRegression1 Perform Linear Regression 2014-04-01 1.0.1
locarna locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile LocARNA - A suite for multiple alignment and folding of RNAs 2015-02-28 http://www.bioinf.uni-freiburg.de/Software/LocARNA/ 2.0.1 locarna 2.0.1 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 36 46 314 350 0 0 0 0 0 0 0 0 36 118 314 978
logistic_regression_vif LogisticRegression Perform Logistic Regression with vif 2014-04-01 1.0.1 numpy To update Sequence Analysis, Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 48 64 173 0 0 0 0 12 72 64 301
maf_cpg_filter cpgFilter Mask CpG/non-CpG sites from MAF file 2014-04-01 1.0.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 28 85 356 0 0 0 0 6 40 85 526
-mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences 2015-06-16 https://mafft.cbrc.jp/alignment/software/ 7.526 mafft 7.525 To update RNA Multiple sequence alignment Multiple sequence alignment Sequence analysis Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 1865 1951 172433 174456 4266 5521 108640 122790 1172 1172 20027 20027 7303 23250 301100 919473
+mafft rbc_mafft_add, rbc_mafft Multiple alignment program for amino acid or nucleotide sequences 2015-06-16 https://mafft.cbrc.jp/alignment/software/ 7.526 mafft 7.525 To update RNA Multiple sequence alignment Multiple sequence alignment Sequence analysis Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/mafft https://github.com/bgruening/galaxytools/tree/master/tools/mafft MAFFT MAFFT MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 1865 1951 172433 174456 4266 5521 108640 122790 1172 1172 20027 20027 7303 23250 301100 919473
mapping_to_ucsc mapToUCSC Format mapping data as UCSC custom track 2014-05-19 1.0.0 To update Visualization, Convert Formats, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mavedb_importer mavedb_importer data source for MaveDB 2023-12-13 0.9 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/ https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 8 8 0 0 0 0 0 0 0 0 2 6 8 24
mea mea Maximum expected accuracy prediction 2015-07-29 http://www.bioinf.uni-leipzig.de/Software/mea 0.6.4.1 mea 0.6.4 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 5 5 73 86 0 0 0 0 0 0 0 0 5 15 73 232
-megablast_xml_parser megablast_xml_parser Parse blast XML output 2014-05-19 1.0.1 python To update Next Gen Mappers, Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 103 141 743 816 82 459 292 2868 0 0 0 0 185 970 1035 5754
-merge gops_merge_1 Merge the overlapping intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 418 441 565922 566630 671 4353 45844 107523 100 137 19828 19994 1189 7309 631594 1957335
-merge_cols mergeCols1 Merge columns together. 2012-12-04 1.0.3 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 1906 2128 20905 31051 885 3172 21780 132833 122 152 1524 1925 2913 11278 44209 254227
+megablast_xml_parser megablast_xml_parser Parse blast XML output 2014-05-19 1.0.1 python To update Next Gen Mappers, Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 103 141 743 816 82 459 292 2868 0 0 0 0 185 970 1035 5754
+merge gops_merge_1 Merge the overlapping intervals of a dataset 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 418 441 565922 566630 671 4353 45844 107523 100 137 19828 19994 1189 7309 631594 1957335
+merge_cols mergeCols1 Merge columns together. 2012-12-04 1.0.3 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 1906 2128 20905 31051 885 3172 21780 132833 122 152 1524 1925 2913 11278 44209 254227
methtools methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling tools for methylation analysis 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0.1.1 methtools To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methtools https://github.com/bgruening/galaxytools/tree/master/tools/methtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 155 453 632 5461 0 0 0 0 0 0 0 0 155 763 632 6725
-methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 2016-12-20 http://bioconductor.org/packages/release/bioc/html/methylKit.html 0.99.2 bioconductor-methylkit 1.28.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-metilene metilene Differential DNA methylation calling 2015-12-14 0.2.6.1 metilene 0.2.8 To update RNA, Statistics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 442 3209 4572 79 79 479 479 51 51 315 315 442 1456 4003 13372
+methylkit methylkit A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. 2016-12-20 http://bioconductor.org/packages/release/bioc/html/methylKit.html 0.99.2 bioconductor-methylkit 1.28.0 To update Epigenetics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/methylkit https://github.com/bgruening/galaxytools/tree/master/tools/methylkit 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+metilene metilene Differential DNA methylation calling 2015-12-14 0.2.6.1 metilene 0.2.8 To update RNA, Statistics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/metilene https://github.com/bgruening/galaxytools/tree/master/tools/metilene 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 312 442 3209 4572 79 79 479 479 51 51 315 315 442 1456 4003 13372
mgnify_seqprep mgnify_seqprep A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines. 2024-05-14 https://github.com/jstjohn/SeqPrep 1.2 To update Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 573 573 0 0 0 0 0 0 0 0 3 9 573 1719
miclip mi_clip Identification of binding sites in CLIP-Seq data. 2015-02-28 https://cran.r-project.org/src/contrib/Archive/MiClip/ 1.2.0 Rscript To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/miclip https://github.com/bgruening/galaxytools/tree/master/tools/miclip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
microsatellite_birthdeath microsatellite_birthdeath Identify microsatellite births and deaths 2013-09-25 1.0.0 To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -390,16 +389,16 @@ microsats_alignment_level microsats_align1 Extract Orthologous Microsatellites f
microsats_mutability microsats_mutability1 Estimate microsatellite mutability by specified attributes 2014-04-01 1.1.0 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 87 34 312 0 0 0 0 22 131 34 380
minced minced MinCED - Mining CRISPRs in Environmental Datasets 2015-02-28 http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README 0.2.0 minced 0.4.2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minced https://github.com/bgruening/galaxytools/tree/master/tools/minced 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 115 124 1213 1309 0 0 0 0 0 0 0 0 115 354 1213 3735
mine maximal_information_based_nonparametric_exploration Maximal Information-based Nonparametric Exploration 2014-07-28 0.0.1 MINE To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 8 9 11 6 19 17 63 0 0 0 0 14 55 26 126
-minipolish minipolish Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.1.3 minipolish 0.1.3 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 229 229 0 0 0 0 0 0 0 0 32 96 229 687
-mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. 2021-05-29 https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 3 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 176 176 1020 1020 73 73 414 414 20 20 277 277 269 807 1711 5133
+minipolish minipolish Polishing miniasm assemblies 2022-10-19 https://github.com/rrwick/Minipolish 0.1.3 minipolish 0.1.3 Up-to-date Sequence Analysis Localised reassembly, Read depth analysis Localised reassembly, Read depth analysis Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/minipolish https://github.com/bgruening/galaxytools/tree/master/tools/minipolish minipolish minipolish 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 229 229 0 0 0 0 0 0 0 0 32 96 229 687
+mitohifi mitohifi Assembly mitogenomes from Pacbio HiFi read. 2021-05-29 https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2 3 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 176 176 1020 1020 73 73 414 414 20 20 277 277 269 807 1711 5133
molecule_to_gspan bg_mol2gspan converter 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0.2 openbabel 2.3.90dev7d621d9 To update Convert Formats bgruening https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
motus mereg_mOTUs_tables, motus_profiler Tool for profiling the abundance of microbial taxa. 2024-09-06 https://github.com/motu-tool/mOTUs 3.1.0 motus 3.1.0 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs https://github.com/bgruening/galaxytools/tree/master/tools/motus mOTUs Metagenomic operational taxonomic units (mOTUs) Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mqc mqc Ribosome profiling mapping quality control tool 2017-08-11 https://github.com/Biobix/mQC 1.9 mqc 1.10 To update Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 9 9 71 76 0 0 0 0 0 0 0 0 9 27 71 218
multispecies_orthologous_microsats multispecies_orthologous_microsats Extract orthologous microsatellites 2013-09-25 1.0.0 bx-sputnik To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mummer mummerplot_wrapper Draw dotplots using mummer, mucmer, or promer with mummerplot 2014-05-22 http://mummer.sourceforge.net/ 0.0.8 ghostscript 9.18 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 199 211 883 921 199 199 730 730 34 49 136 202 432 1323 1749 5351
-music music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) 2021-09-12 https://github.com/xuranw/MuSiC 0.1.1 music-deconvolution 0.1.1 Up-to-date Transcriptomics, Single Cell bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution music_deconvolution MuSiC Deconvolution MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 289 289 2801 2801 80 80 364 364 21 21 1357 1357 390 1170 4522 13566
+music music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution Multi-subject Single Cell deconvolution (MuSiC) 2021-09-12 https://github.com/xuranw/MuSiC 0.1.1 music-deconvolution 0.1.1 Up-to-date Transcriptomics, Single Cell bgruening https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution music_deconvolution MuSiC Deconvolution MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another. 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 289 289 2801 2801 80 80 364 364 21 21 1357 1357 390 1170 4522 13566
mutate_snp_codon mutate_snp_codon_1 Mutate Codons with SNPs 2013-09-25 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5 5 44 49 23 118 81 417 0 0 0 0 28 179 125 716
-nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. 2018-05-28 https://github.com/jts/nanopolish 0.14.0 nanopolish 0.14.0 Up-to-date bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 215 229 9284 9694 0 0 0 0 49 49 2358 2358 264 806 11642 35336
+nanopolish nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data. 2018-05-28 https://github.com/jts/nanopolish 0.14.0 nanopolish 0.14.0 Up-to-date bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish 0 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 215 229 9284 9694 0 0 0 0 49 49 2358 2358 264 806 11642 35336
nastiseq nastiseq A method to identify cis-NATs using ssRNA-seq 2017-02-21 https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ 1.0 r-nastiseq 1.0 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 1 36 40 0 0 0 0 0 0 0 0 1 3 36 112
netboxr netboxr netboxr enables automated discovery of biological process modules by network analysis 2022-08-24 1.6.0 bioconductor-netboxr 1.9.0 To update Systems Biology bgruening https://github.com/bgruening/galaxytools/tree/master/tools/netboxr 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 12 12 0 0 0 0 0 0 0 0 6 18 12 36
nextdenovo nextdenovo String graph-based de novo assembler for long reads 2023-02-09 https://github.com/Nextomics/NextDenovo 2.5.0 nextdenovo 2.5.2 To update Assembly De-novo assembly, Genome assembly De-novo assembly, Genome assembly Sequencing, Sequence assembly Sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo nextdenovo NextDenovo "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." 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 158 158 391 391 0 0 0 0 0 0 0 0 158 474 391 1173
@@ -417,8 +416,8 @@ pgsnp2gd_snp pgSnp2gd_snp Convert from pgSnp to gd_snp 2014-07-28 1.0.0 To up
pgtools pg_dump, pg_import, pg_query tool suite for dealing with Postgresql databases from Galaxy's history 2017-09-28 https://www.postgresql.org postgresql To update Data Export, Data Source bgruening https://github.com/bgruening/galaxytools/tools/pgtools https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pharmcat pharmcat Pharmacogenomics Clinical Annotation Tool 2022-01-28 https://pharmcat.org/ To update Variant Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 109 109 84 84 250 250 0 0 0 0 113 339 359 1077
pileometh pileometh A tool for processing bisulfite sequencing alignments 2017-02-14 https://github.com/dpryan79/MethylDackel 0.5.2 methyldackel 0.6.1 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 638 894 14907 18971 230 230 2677 2677 83 83 2313 2313 951 3109 19897 63755
-pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases 2015-03-06 1.0.3 bx-python 0.13.0 To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 48 54 613 640 201 1552 1381 7804 22 30 756 815 271 2178 2750 14759
-pileup_parser pileup_parser Filter pileup on coverage and SNPs 2013-08-26 https://github.com/galaxyproject/tools-devteam/ 1.0.2 perl To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 414 461 3639 3774 1247 4531 9754 52522 191 318 1893 2433 1852 9014 15286 89301
+pileup_interval pileup_interval Pileup-to-Interval condenses pileup format into ranges of bases 2015-03-06 1.0.3 bx-python 0.13.0 To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 48 54 613 640 201 1552 1381 7804 22 30 756 815 271 2178 2750 14759
+pileup_parser pileup_parser Filter pileup on coverage and SNPs 2013-08-26 https://github.com/galaxyproject/tools-devteam/ 1.0.2 perl To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 414 461 3639 3774 1247 4531 9754 52522 191 318 1893 2433 1852 9014 15286 89301
pipmir pipmir A method to identify novel plant miRNA. 2016-11-25 https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ 0.1.0 pipmir 1.1 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 42 45 238 283 0 0 0 0 0 0 0 0 42 129 238 759
piranha piranha Piranha is a peak-caller for CLIP- and RIP-Seq data 2015-07-02 1.2.1.0 piranha 1.2.1 To update Sequence Analysis, RNA rnateam https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha https://github.com/bgruening/galaxytools/tree/master/tools/piranha 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 94 119 1408 2068 0 0 0 0 0 0 0 0 94 307 1408 4884
platypus bg_platypus efficient and accurate variant-detection in high-throughput sequencing data 2015-02-28 http://www.well.ox.ac.uk/platypus 0.0.11 platypus To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/platypus https://github.com/bgruening/galaxytools/tree/master/tools/platypus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -434,15 +433,15 @@ protein_properties bg_protein_properties Calculation of various properties from
proteomics_improviser proteomics_improviser Visualisation of PepXML files 2015-02-28 http://www.improviser.uni-freiburg.de/ 1.1.0.1 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pubchem_rest_tool pubchem_rest_tool This tool fetches data from pubchem via the PubChem REST API. 2015-02-28 https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html 0.1.0 To update Data Source bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
quality_filter qualityFilter Filter nucleotides based on quality scores 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 35 62 98 724 0 0 0 0 35 132 98 920
-racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 839 850 27113 27315 475 475 9089 9089 171 171 5452 5452 1485 4466 41654 125164
+racon racon Consensus module for raw de novo DNA assembly of long uncorrected reads. 2018-06-11 https://github.com/isovic/racon 1.5.0 racon 1.5.0 Up-to-date Sequence Analysis Genome assembly, Mapping assembly Genome assembly, Mapping assembly Whole genome sequencing, Sequence assembly Whole genome sequencing, Sequence assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/racon https://github.com/bgruening/galaxytools/tree/master/tools/racon Racon Racon 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 839 850 27113 27315 475 475 9089 9089 171 171 5452 5452 1485 4466 41654 125164
rbpbench rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 2023-12-03 https://github.com/michauhl/RBPBench 0.8.1 rbpbench 1.0.1 To update Sequence Analysis, RNA, CLIP-seq RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 90 90 0 0 0 0 0 0 0 0 6 18 90 270
rcas rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments 2017-04-13 https://github.com/BIMSBbioinfo/RCAS 1.5.4 bioconductor-rcas 1.28.2 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 88 98 860 1257 0 0 0 0 0 0 0 0 88 274 860 2977
rcve rcve1 Compute RCVE 2014-04-01 1.0.0 R To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 46 49 191 0 0 0 0 5 56 49 289
reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. 2015-12-09 https://github.com/chengyuan/reago-1.1 1.1 reago 1.1 Up-to-date Metagenomics, RNA Sequence assembly Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Sequence assembly, RNA, Metagenomics, Microbiology rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-remove_beginning Remove beginning1 Remove lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 3525 3682 148572 169964 3910 8163 36694 113826 1475 1598 9713 10577 8910 31263 194979 684325
+remove_beginning Remove beginning1 Remove lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 3525 3682 148572 169964 3910 8163 36694 113826 1475 1598 9713 10577 8910 31263 194979 684325
remurna remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 2016-11-24 https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna 1.0.0 remurna 1.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 7 39 44 0 0 0 0 0 0 0 0 6 19 39 122
repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2015-02-28 http://www.repeatmasker.org/ 0.1.2 RepeatMasker 4.0.9_p2 To update Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 810 810 5998 5998 803 803 7618 7618 292 292 3135 3135 1905 5715 16751 50253
-replace_column_by_key_value_file replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. 2017-02-24 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 463 492 577184 577312 283 373 43900 44233 112 112 2190 2190 858 2693 623274 1870283
+replace_column_by_key_value_file replace_column_with_key_value_file A tool to replace all column entries of a file given by values of a key-value file. 2017-02-24 0.2 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 463 492 577184 577312 283 373 43900 44233 112 112 2190 2190 858 2693 623274 1870283
ribotaper ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling A method for defining traslated ORFs using Ribosome Profiling data. 2016-06-07 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ 1.3.1a ribotaper 1.3.1 To update RNA Gene expression profiling Gene expression profiling Functional genomics Functional genomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper ribotaper RiboTaper New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 78 78 661 681 0 0 0 0 0 0 0 0 78 234 661 2003
rmap rmap_wrapper RMAP for Solexa Short Reads Alignment 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rmapq rmapq_wrapper RMAPQ for Solexa Short Reads Alignment with Quality Scores 2014-05-19 1.0.0 rmap 2.1 To update Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -460,162 +459,163 @@ sailfish sailfish Sailfish is a tool for transcript quantification from RNA-seq
sam2interval sam2interval Convert SAM to interval. 2013-08-26 1.0.2 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 63 1155 1251 189 1748 2264 18187 10 17 525 590 256 2340 3944 27916
sam_bitwise_flag_filter sam_bw_filter Filter SAM on bitwise flag values 2013-08-26 1.0.1 python To update SAM devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 12 26 96 278 450 6346 3554 76029 16 29 229 345 478 7357 3879 84410
sambamba sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort Sambamba: process your BAM data faster! 2016-06-23 https://github.com/biod/sambamba 1.0.1 sambamba 1.0.1 Up-to-date SAM bgruening https://github.com/biod/sambamba https://github.com/bgruening/galaxytools/tree/master/tools/sambamba 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 51 297 297 0 0 0 0 0 0 0 0 51 153 297 891
-sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 340 382 3421 3859 109 109 883 883 15 15 1138 1138 464 1434 5442 16764
+sample_seqs sample_seqs Sub-sample sequences files (e.g. to reduce coverage) 2014-02-18 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 0.2.6 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 340 382 3421 3859 109 109 883 883 15 15 1138 1138 464 1434 5442 16764
samtools_depad samtools_depad Re-align a SAM/BAM file with a padded reference (using samtools depad) 2014-04-14 http://www.htslib.org/ 0.0.5 samtools 1.21 To update Assembly, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-samtools_depth samtools_depth Coverage depth via samtools 2014-11-19 http://www.htslib.org/ 0.0.3 samtools 1.21 To update Assembly, Sequence Analysis, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 720 726 6485 6549 1518 1518 10127 10127 37 37 238 238 2275 6831 16850 50614
-samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) 2013-11-11 http://www.htslib.org/ 0.0.6 samtools 1.21 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4053 4497 52099 55110 6930 9936 73194 108684 1222 1419 14771 15714 12205 40262 140064 459636
-scatterplot scatterplot_rpy Scatterplot of two numeric columns 2014-07-28 1.0.3 numpy To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 179 261 1234 1752 231 1927 680 9223 0 18 0 49 410 3026 1914 14852
+samtools_depth samtools_depth Coverage depth via samtools 2014-11-19 http://www.htslib.org/ 0.0.3 samtools 1.21 To update Assembly, Sequence Analysis, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 720 726 6485 6549 1518 1518 10127 10127 37 37 238 238 2275 6831 16850 50614
+samtools_idxstats samtools_idxstats BAM mapping statistics (using samtools idxstats) 2013-11-11 http://www.htslib.org/ 0.0.6 samtools 1.21 To update Assembly, Next Gen Mappers, SAM peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4053 4497 52099 55110 6930 9936 73194 108684 1222 1419 14771 15714 12205 40262 140064 459636
+scatterplot scatterplot_rpy Scatterplot of two numeric columns 2014-07-28 1.0.3 numpy To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 179 261 1234 1752 231 1927 680 9223 0 18 0 49 410 3026 1914 14852
sed_wrapper sed_stream_editor Manipulate your data with the sed command line tool. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/sed 0.0.1 sed To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sed https://github.com/bgruening/galaxytools/tree/master/tools/sed 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 53 281 2284 0 0 0 0 0 0 0 0 10 73 281 2846
segemehl segemehl segemehl - short read mapping with gaps 2015-02-28 http://www.bioinf.uni-leipzig.de/Software/segemehl/ 0.2.0.4 segemehl 0.3.4 To update Next Gen Mappers rnateam https://github.com/bgruening/galaxytools/tree/master/tools/segemehl https://github.com/bgruening/galaxytools/tree/master/tools/segemehl 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 98 113 1095 1306 0 0 0 0 0 0 0 0 98 309 1095 3496
-selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format 2017-03-11 https://github.com/eggzilla/SelectSequences 1.0.5 selectsequencesfrommsa 1.0.5 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 50 305 463 0 0 0 0 0 0 0 0 43 136 305 1073
+selectsequencesfrommsa selectsequencesfrommsa SelectSequences - selects representative entries from a multiple sequence alignment in clustal format 2017-03-11 https://github.com/eggzilla/SelectSequences 1.0.5 selectsequencesfrommsa 1.0.5 Up-to-date RNA, Sequence Analysis rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 43 50 305 463 0 0 0 0 0 0 0 0 43 136 305 1073
seq_composition seq_composition Sequence composition 2014-08-12 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 0.0.5 biopython 1.70 To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 137 195 1053 1186 206 206 680 680 0 0 0 0 343 1087 1733 5332
-seq_filter_by_id seq_filter_by_id Filter sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 732 799 30300 32553 619 621 21726 31891 144 144 2886 2886 1495 4554 54912 177154
-seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files 2014-11-04 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 180 205 4322 4714 0 0 0 0 0 0 0 0 180 565 4322 13358
-seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) 2018-05-08 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 To update Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+seq_filter_by_id seq_filter_by_id Filter sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 0.2.9 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 732 799 30300 32553 619 621 21726 31891 144 144 2886 2886 1495 4554 54912 177154
+seq_filter_by_mapping seq_filter_by_mapping Filter sequencing reads using SAM/BAM mapping files 2014-11-04 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0.0.8 biopython 1.70 To update Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 180 205 4322 4714 0 0 0 0 0 0 0 0 180 565 4322 13358
+seq_length seq_length Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc) 2018-05-08 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0.0.5 biopython 1.70 To update Fasta Manipulation, Fastq Manipulation, Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
seq_primer_clip seq_primer_clip Trim off 5' or 3' primers 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0.0.18 galaxy_sequence_utils 1.2.0 To update Assembly, Fasta Manipulation, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-seq_rename seq_rename Rename sequences with ID mapping from a tabular file 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-seq_select_by_id seq_select_by_id Select sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 260 289 2196 3529 260 809 2196 7921
+seq_rename seq_rename Rename sequences with ID mapping from a tabular file 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.2.0 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+seq_select_by_id seq_select_by_id Select sequences by ID 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 To update Fasta Manipulation, Sequence Analysis, Text Manipulation peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 260 289 2196 3529 260 809 2196 7921
short_reads_figure_high_quality_length hist_high_quality_score Histogram of high quality score reads 2014-05-19 1.0.0 rpy To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
short_reads_figure_score quality_score_distribution Build base quality distribution 2014-05-19 1.0.2 fontconfig To update Sequence Analysis, Graphics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 25 30 145 163 23 711 196 3360 0 0 0 0 48 837 341 4205
short_reads_trim_seq trim_reads Select high quality segments 2014-05-19 1.0.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 51 60 175 220 85 1602 350 6657 0 0 0 0 136 1934 525 7927
-show_beginning Show beginning1 Select lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 2184 2789 27232 36366 4191 18767 16648 84460 373 452 2785 3276 6748 35504 46665 217432
-show_tail Show tail1 Select lines from the end of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 378 589 1620 2660 682 1851 10551 24579 67 83 284 398 1127 4777 12455 52547
-sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions 2014-01-27 https://home.gwu.edu/~wpeng/Software.htm 1.1 SICER 1.1 Up-to-date ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30 42 276 379 146 1008 972 9053 5 7 644 689 181 1419 1892 13905
+show_beginning Show beginning1 Select lines from the beginning of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 2184 2789 27232 36366 4191 18767 16648 84460 373 452 2785 3276 6748 35504 46665 217432
+show_tail Show tail1 Select lines from the end of a file. 2012-12-04 1.0.0 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 0 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 378 589 1620 2660 682 1851 10551 24579 67 83 284 398 1127 4777 12455 52547
+sicer peakcalling_sicer Statistical approach for the Identification of ChIP-Enriched Regions 2014-01-27 https://home.gwu.edu/~wpeng/Software.htm 1.1 SICER 1.1 Up-to-date ChIP-seq devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 30 42 276 379 146 1008 972 9053 5 7 644 689 181 1419 1892 13905
sklearn sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split Machine Learning tool suite from Scikit-learn 2016-05-02 http://scikit-learn.org 1.0.11.0 To update Machine Learning, Statistics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sklearn https://github.com/bgruening/galaxytools/tree/master/tools/sklearn 30 14 31 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 31 27 0 2402 2666 82169 116810 2375 2375 18101 18101 321 321 17549 17549 5098 15558 117819 388098
snpfreq hgv_snpFreq snpFreq significant SNPs in case-control data 2014-07-28 1.0.1 R To update Variant Analysis, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 10 12 35 44 68 181 307 649 16 23 227 260 94 404 569 2091
-sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 4.3.6 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1047 1126 19865 21034 328 328 3141 3141 189 189 3304 3304 1564 4771 26310 80099
-split_file_on_column tp_split_on_column Split a file on a specific column. 2015-02-28 0.6 gawk To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 408 453 5995 6261 311 311 2150 2150 2 2 26 26 721 2208 8171 24779
-split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. 2018-07-10 https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 968 984 16415 16623 672 672 9133 9133 148 148 4140 4140 1788 5380 29688 89272
-split_paired_reads split_paired_reads Split paired end reads 2013-09-25 1.0.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 13 31 66 200 384 31 131 200 797
-splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences 2015-10-16 0.4.0 biopython 1.70 To update Text Manipulation rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 278 294 1772 1811 564 564 3012 3012 0 0 0 0 842 2542 4784 14391
+sortmerna bg_sortmerna SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers. 2015-02-28 http://bioinfo.lifl.fr/RNA/sortmerna/ 4.3.6 sortmerna 4.3.7 To update RNA Sequence similarity search, Sequence comparison, Sequence alignment analysis Sequence similarity search, Sequence alignment analysis Metatranscriptomics, Metagenomics Metatranscriptomics, Metagenomics rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna sortmerna SortMeRNA Sequence analysis tool for filtering, mapping and OTU-picking NGS reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1047 1126 19865 21034 328 328 3141 3141 189 189 3304 3304 1564 4771 26310 80099
+split_file_on_column tp_split_on_column Split a file on a specific column. 2015-02-28 0.6 gawk To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 408 453 5995 6261 311 311 2150 2150 2 2 26 26 721 2208 8171 24779
+split_file_to_collection split_file_to_collection Split tabular, MGF, FASTA, or FASTQ files to a dataset collection. 2018-07-10 https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 0.5.2 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 968 984 16415 16623 672 672 9133 9133 148 148 4140 4140 1788 5380 29688 89272
+split_paired_reads split_paired_reads Split paired end reads 2013-09-25 1.0.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 13 31 66 200 384 31 131 200 797
+splitfasta rbc_splitfasta Split a multi-sequence fasta file into files containing single sequences 2015-10-16 0.4.0 biopython 1.70 To update Text Manipulation rnateam https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 278 294 1772 1811 564 564 3012 3012 0 0 0 0 842 2542 4784 14391
sshmm sshmm ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data 2018-07-05 https://github.molgen.mpg.de/heller/ssHMM 1.0.7 sshmm 1.0.7 Up-to-date Sequence Analysis, RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 17 18 214 225 0 0 0 0 0 0 0 0 17 52 214 653
stats_perf_tool stats_perf_tool suitable for boolean classification problems 2015-02-28 http://osmot.cs.cornell.edu/kddcup/software.html 5.11.0 perf To update bgruening https://github.com/bgruening/galaxytools/tree/master/tools/perf https://github.com/bgruening/galaxytools/tree/master/tools/perf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
stress_ng stress_ng stress test a computer system in various selectable ways 2021-03-04 0.12.04 stress-ng To update Web Services bgruening-util https://github.com/ColinIanKing/stress-ng https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 62 62 0 0 0 0 0 0 0 0 3 9 62 186
structure_to_gspan structure_to_gspan Convert RNA structure to GSPAN graphs 2017-05-18 0.4 graphclust-wrappers 0.6.0 To update RNA rnateam https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 50 62 991 3060 0 0 0 0 0 0 0 0 50 162 991 5042
substitution_rates subRate1 Estimate substitution rates for non-coding regions 2014-04-01 1.0.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 747 121 3901 4 4 105 114 38 827 226 4467
substitutions substitutions1 Fetch substitutions from pairwise alignments 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 84 93 901 0 0 0 0 13 110 93 1087
-subtract gops_subtract_1 Subtract the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 410 470 566512 567199 1473 7631 49985 184650 155 188 20648 20897 2038 12365 637145 2047036
+subtract gops_subtract_1 Subtract the intervals of two datasets 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 410 470 566512 567199 1473 7631 49985 184650 155 188 20648 20897 2038 12365 637145 2047036
subtract_query subtract_query1 Subtract Whole Dataset from another dataset 2014-04-01 https://github.com/galaxyproject/gops 0.1 bx-python 0.13.0 To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 124 141 1178 1450 636 3435 3169 40539 26 38 799 950 786 5186 5146 53231
-t2ps Draw_phylogram Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 68 90 411 472 13 1240 102 7952 0 0 0 0 81 1492 513 9450
-t2t_report t2t_report Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 78 927 959 18 1143 130 7194 0 0 0 0 83 1387 1057 10267
+t2ps Draw_phylogram Draw phylogeny 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics Phylogenetic tree visualisation Phylogenetic tree visualisation Phylogenomics Phylogenomics devteam https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps t2ps Draw phylogeny """Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper" 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 68 90 411 472 13 1240 102 7952 0 0 0 0 81 1492 513 9450
+t2t_report t2t_report Summarize taxonomy 2014-01-27 https://bitbucket.org/natefoo/taxonomy 1.0.0 taxonomy 0.10.0 To update Metagenomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 65 78 927 959 18 1143 130 7194 0 0 0 0 83 1387 1057 10267
t_test_two_samples t_test_two_samples T Test for Two Samples 2013-09-25 1.0.1 R To update Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 20 31 141 215 79 274 520 1166 11 12 1025 1118 110 537 1686 5871
table_annovar table_annovar Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered 2013-12-02 0.2 annovar To update Variant Analysis devteam Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2803 7456 16526 64515 0 0 0 0 2803 13062 16526 97567
tables_arithmetic_operations tables_arithmetic_operations Arithmetic Operations on tables 2014-04-01 https://github.com/galaxyproject/gops 1.0.0 perl To update Genomic Interval Operations devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 33 38 2188 2220 0 0 0 0 0 0 0 0 33 104 2188 6596
-tabular_to_fasta tab2fasta Tabular-to-FASTA 2014-05-19 1.1.1 python To update Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1489 1702 329032 333057 2441 8587 79033 215770 296 360 27876 33727 4226 19101 435941 1454436
+tabular_to_fasta tab2fasta Tabular-to-FASTA 2014-05-19 1.1.1 python To update Convert Formats devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1489 1702 329032 333057 2441 8587 79033 215770 296 360 27876 33727 4226 19101 435941 1454436
tapscan tapscan_classify Search for transcription associated proteins (TAPs) 2024-02-14 https://plantcode.cup.uni-freiburg.de/tapscan/ 4.76+galaxy0 hmmer 3.4 To update Proteomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 19 19 0 0 0 0 0 0 0 0 6 18 19 57
targetfinder targetfinder Plant small RNA target prediction tool 2015-10-23 https://github.com/carringtonlab/TargetFinder.git 1.7 targetfinder 1.7 Up-to-date RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 89 92 827 838 41 41 114 114 29 29 900 900 159 480 1841 5534
-text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. 2015-02-28 https://www.gnu.org/software/ 9.3 coreutils 8.25 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 20 20 20 20 0 0 0 0 0 0 0 0 0 0 19 1 19 0 0 0 0 0 0 20 0 0 0 0 0 0 19 19 19 0 37698 42095 3898014 4015573 47636 69828 648268 915282 7778 7953 103365 105214 93112 306100 4649647 14335363
+text_processing tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq High performance text processing tools using the GNU coreutils, sed, awk and friends. 2015-02-28 https://www.gnu.org/software/ 9.3 coreutils 8.25 To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing 20 20 20 20 0 0 0 0 0 0 0 0 0 0 0 19 1 19 0 0 0 0 0 20 0 0 0 0 0 0 19 19 19 0 37698 42095 3898014 4015573 47636 69828 648268 915282 7778 7953 103365 105214 93112 306100 4649647 14335363
tgsgapcloser tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. 2021-11-14 https://github.com/BGI-Qingdao/TGS-GapCloser 1.0.3 tgsgapcloser 1.2.1 To update Assembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 51 51 547 547 0 0 0 0 0 0 0 0 51 153 547 1641
tiara tiara Tool for identification of eukaryotic sequences in the metagenomic datasets. 2024-05-23 https://github.com/ibe-uw/tiara 1.0.3 tiara To update Metagenomics, Sequence Analysis Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection Sequencing, Genomics, DNA polymorphism, DNA structural variation Sequencing, Genomics, DNA polymorphism bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tiara https://github.com/bgruening/galaxytools/tree/master/tools/tiara Tiara TIARA Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 15 15 0 0 0 0 0 0 0 0 8 24 15 45
tmhmm_and_signalp promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb 2010-10-21 https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0.0.13 promoter To update Sequence Analysis peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 1137 1278 11743 12752 1 1 2 2 0 0 0 0 1138 3555 11745 36244
tophat tophat Tophat for Illumina 2014-01-27 1.5.0 samtools 1.21 To update RNA, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 28 7228 158 66524 0 0 0 0 28 7285 158 66841
-tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads 2014-01-27 http://ccb.jhu.edu/software/tophat/index.shtml 2.1.1 bowtie2 2.5.4 To update RNA, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1076 1664 15496 26623 8372 27829 83063 343017 508 1012 5388 14057 9956 50417 103947 591591
+tophat2 tophat2 Tophat - fast splice junction mapper for RNA-Seq reads 2014-01-27 http://ccb.jhu.edu/software/tophat/index.shtml 2.1.1 bowtie2 2.5.4 To update RNA, Next Gen Mappers devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1076 1664 15496 26623 8372 27829 83063 343017 508 1012 5388 14057 9956 50417 103947 591591
tophat_fusion_post tophat_fusion_post Wrapper for Tophat-Fusion post step 2014-01-27 0.1 blast+ To update Transcriptomics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 41 46 220 242 2 191 6 814 8 12 100 120 51 351 326 1828
-trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer 2015-02-28 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 0.6.7 trim-galore 0.6.10 To update Sequence Analysis, Fastq Manipulation Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore trim_galore Trim Galore 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5733 6500 229489 275008 11708 16638 228708 324716 1439 1527 22644 23869 18880 62425 480841 1585275
-trimmer trimmer Trim leading or trailing characters. 2012-12-04 0.0.1 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 1 1 1 1 447 512 5304 7438 658 2946 15698 108672 53 81 266 822 1158 5855 21268 159468
-trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. 2015-02-28 http://mbioserv2.mbioekol.lu.se/ARAGORN/ 0.6 aragorn 1.2.41 To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 741 807 4361 4601 0 0 0 0 190 190 2469 2469 931 2859 6830 20730
+trim_galore trim_galore Trim Galore adaptive quality and adapter trimmer 2015-02-28 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 0.6.7 trim-galore 0.6.10 To update Sequence Analysis, Fastq Manipulation Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Sequence analysis Sequence analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore trim_galore Trim Galore 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 5733 6500 229489 275008 11708 16638 228708 324716 1439 1527 22644 23869 18880 62425 480841 1585275
+trimmer trimmer Trim leading or trailing characters. 2012-12-04 0.0.1 To update Text Manipulation devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 1 1 447 512 5304 7438 658 2946 15698 108672 53 81 266 822 1158 5855 21268 159468
+trna_prediction aragorn_trna, trnascan Aragorn predicts tRNA and tmRNA in nucleotide sequences. 2015-02-28 http://mbioserv2.mbioekol.lu.se/ARAGORN/ 0.6 aragorn 1.2.41 To update RNA bgruening https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 0 2 2 0 741 807 4361 4601 0 0 0 0 190 190 2469 2469 931 2859 6830 20730
ucsc_custom_track build_ucsc_custom_track_1 Build custom track for UCSC genome browser 2014-07-28 1.0.1 python To update Sequence Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 151 373 463 638 4080 2249 18611 0 0 0 0 772 5775 2622 24318
uniprot_rest_interface uniprot UniProt ID mapping and sequence retrieval 2015-10-09 https://github.com/jdrudolph/uniprot 0.6 requests To update Proteomics, Sequence Analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 341 412 2117 2725 594 1011 3111 5779 50 50 806 806 985 3443 6034 21378
-unique bg_uniq This tool returns all unique lines from a tab-separated file. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 554 612 6690 8818 0 0 0 0 0 0 0 0 554 1720 6690 22198
+unique bg_uniq This tool returns all unique lines from a tab-separated file. 2015-02-28 https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0.4 python To update Text Manipulation bgruening https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 554 612 6690 8818 0 0 0 0 0 0 0 0 554 1720 6690 22198
varscan_version_2 varscan VarScan wrapper 2013-11-17 https://dkoboldt.github.io/varscan/ 2.4.2 varscan 2.4.6 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 606 699 5058 6139 2965 5686 17232 53268 424 482 2298 2656 3995 14857 24588 111239
vcf2pgsnp vcf2pgSnp VCF to pgSnp 2014-07-28 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 57 65 191 221 209 584 1399 2700 0 0 0 0 266 1181 1590 6101
vcf_annotate vcf_annotate Annotate a VCF file (dbSNP, hapmap) 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 1 31 54 263 340 31 118 263 868
-vcf_extract vcf_extract Extract reads from a specified region 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 513 569 6 21 513 1595
+vcf_extract vcf_extract Extract reads from a specified region 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 513 569 6 21 513 1595
vcf_filter vcf_filter Filter a VCF file 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 129 140 400 455 0 0 0 0 19 56 238 606 148 492 638 2337
-vcf_intersect vcf_intersect Generate the intersection of two VCF files 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 19 0 0 0 0 19 28 335 463 19 69 335 1152
+vcf_intersect vcf_intersect Generate the intersection of two VCF files 2014-01-27 1.0.0 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 19 0 0 0 0 19 28 335 463 19 69 335 1152
vcftools_annotate vcftools_annotate Annotate VCF using custom/user-defined annotations 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 81 90 155 192 581 1280 1853 3943 13 16 144 156 675 2736 2152 8595
vcftools_compare vcftools_compare Compare VCF files to get overlap and uniqueness statistics 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 142 440 594 0 0 0 0 0 12 0 16 127 408 440 1490
-vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence 2016-10-16 https://vcftools.github.io/ 0.1.11 samtools 1.21 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-vcftools_isec vcftools_isec Intersect multiple VCF datasets 2013-11-24 https://vcftools.github.io/ 0.1.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 104 118 379 537 0 1 0 1 28 48 39 496 132 431 418 1870
+vcftools_consensus vcftools_consensus Apply VCF variants to a fasta file to create consensus sequence 2016-10-16 https://vcftools.github.io/ 0.1.11 samtools 1.21 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+vcftools_isec vcftools_isec Intersect multiple VCF datasets 2013-11-24 https://vcftools.github.io/ 0.1.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 104 118 379 537 0 1 0 1 28 48 39 496 132 431 418 1870
vcftools_merge vcftools_merge Merge multiple VCF datasets into a single dataset 2013-11-24 https://vcftools.github.io/ 0.1.11 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 244 273 817 1084 0 0 0 0 44 60 93 448 288 909 910 3352
vcftools_slice vcftools_slice Subset VCF dataset by genomic regions 2013-11-24 https://vcftools.github.io/ 0.1 echo To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 56 60 410 423 133 362 6261 8115 10 19 127 157 199 839 6798 22291
vcftools_subset vcftools_subset Select samples from a VCF dataset 2013-11-24 https://vcftools.github.io/ 0.1 tabix 1.11 To update Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 46 49 134 142 0 0 0 0 12 19 120 142 58 184 254 792
-venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 667 730 4519 5476 986 2010 9858 18420 0 0 0 0 1653 6046 14377 52650
+venn_list venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc 2013-09-26 https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.2.0 To update Graphics, Sequence Analysis, Visualization peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 667 730 4519 5476 986 2010 9858 18420 0 0 0 0 1653 6046 14377 52650
viennarna viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures 2015-02-28 http://www.tbi.univie.ac.at/RNA/ 2.2.10 viennarna 2.7.0 To update RNA rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 0 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 21 0 344 415 3197 8107 0 0 0 0 0 0 0 0 344 1103 3197 14501
vt vt_@BINARY@, vt_@BINARY@ A tool set for short variant discovery in genetic sequence data. 2015-02-28 0.2 vt 2015.11.10 To update Sequence Analysis, Variant Analysis bgruening https://github.com/atks/vt https://github.com/bgruening/galaxytools/tree/master/tools/vt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
weightedaverage wtavg Assign weighted-average of the values of features overlapping an interval 2014-04-01 1.0.1 galaxy-ops 1.1.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 75 227 2307 0 0 0 0 17 109 227 2761
whisper whisper Transcribe audio or video files to text using the OpenAI Whisper. 2024-04-23 https://github.com/bgruening/galaxytools/tree/master/tools/whisper 20231117 To update Machine Learning bgruening https://github.com/bgruening/galaxytools/tree/master/tools/whisper https://github.com/bgruening/galaxytools/tree/master/tools/whisper 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 96 96 0 0 0 0 0 0 0 0 13 39 96 288
windowsplitter winSplitter Make windows 2014-04-01 1.0.1 bx-python 0.13.0 To update Sequence Analysis, Variant Analysis devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 11 34 328 171 3961 0 0 0 0 34 398 171 4314
-wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. 2018-06-12 https://github.com/ruanjue/wtdbg2 2.5 wtdbg 2.5 Up-to-date Assembly Genome assembly, De-novo assembly Genome assembly, De-novo assembly Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg wtdbg2 wtdbg2 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. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 337 376 1619 1715 0 0 0 0 0 0 0 0 337 1050 1619 4953
-xy_plot XY_Plot_1 Plotting tool for multiple series and graph types 2013-09-25 1.0.2 r-base To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1 1 1 1 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 768 889 4490 6169 1921 3653 6120 15516 556 590 2033 2212 3245 11622 12643 49183
- alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. 2016-03-21 https://github.com/COMBINE-lab/salmon 1.10.1 salmon 1.10.3 To update Sequence Analysis, RNA, Transcriptomics, Single Cell Sequence composition calculation, RNA-Seq quantification, Gene expression analysis Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics RNA-Seq, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data 2 2 3 1 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 2243 2319 73085 77081 3402 4726 90634 122835 513 586 13371 15818 6158 19947 177090 569914
-AMRFinderPlus amrfinderplus """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." 2023-05-12 https://github.com/ncbi/amr 3.12.8 ncbi-amrfinderplus 4.0.3 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus amrfinderplus AMRFinderPlus "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" 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 334 334 5734 5734 106 106 1035 1035 0 0 0 0 440 1320 6769 20307
+wordcloud wordcloud A little word cloud generator in Python. 2024-12-13 https://github.com/amueller/word_cloud 1.9.4 wordcloud To update Visualization bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+wtdbg wtdbg WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly. 2018-06-12 https://github.com/ruanjue/wtdbg2 2.5 wtdbg 2.5 Up-to-date Assembly Genome assembly, De-novo assembly Genome assembly, De-novo assembly Sequence assembly, Sequencing Sequence assembly, Sequencing bgruening https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg wtdbg2 wtdbg2 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. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 337 376 1619 1715 0 0 0 0 0 0 0 0 337 1050 1619 4953
+xy_plot XY_Plot_1 Plotting tool for multiple series and graph types 2013-09-25 1.0.2 r-base To update Graphics, Statistics devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 768 889 4490 6169 1921 3653 6120 15516 556 590 2033 2212 3245 11622 12643 49183
+ alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. 2016-03-21 https://github.com/COMBINE-lab/salmon 1.10.1 salmon 1.10.3 To update Sequence Analysis, RNA, Transcriptomics, Single Cell Sequence composition calculation, RNA-Seq quantification, Gene expression analysis Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics RNA-Seq, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data 2 2 3 1 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 2243 2319 73085 77081 3402 4726 90634 122835 513 586 13371 15818 6158 19947 177090 569914
+AMRFinderPlus amrfinderplus """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." 2023-05-12 https://github.com/ncbi/amr 3.12.8 ncbi-amrfinderplus 4.0.3 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus amrfinderplus AMRFinderPlus "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" 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 334 334 5734 5734 106 106 1035 1035 0 0 0 0 440 1320 6769 20307
Beacon2_Import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. 2024-07-22 https://pypi.org/project/beacon2-import/ 2.2.4 beacon2-import 2.2.4 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 22 22 0 0 0 0 0 0 0 0 7 21 22 66
-ISEScan isescan """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.""" 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.2.3 isescan 1.7.2.1 To update Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 151 151 59386 59386 1 1 56 56 59 59 4741 4741 211 633 64183 192549
-abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes 2016-07-29 https://github.com/tseemann/abricate 1.0.1 abricate 1.0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Genomics, Microbiology Genomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 4097 4130 619817 622353 2915 2915 320454 320454 2012 2227 496156 503743 9024 27320 1436427 4319404
+ISEScan isescan """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.""" 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.2.3 isescan 1.7.2.3 Up-to-date Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 151 151 59386 59386 1 1 56 56 59 59 4741 4741 211 633 64183 192549
+abricate abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes 2016-07-29 https://github.com/tseemann/abricate 1.0.1 abricate 1.0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Genomics, Microbiology Genomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 4097 4130 619817 622353 2915 2915 320454 320454 2012 2227 496156 503743 9024 27320 1436427 4319404
abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes 2023-04-03 https://zenodo.org/record/7370628 1.0.19 abritamr 1.0.19 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr abritamr abriTAMR 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 109 109 1139 1139 0 0 0 0 0 0 0 0 109 327 1139 3417
-abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 http://www.bcgsc.ca/platform/bioinfo/software/abyss 2.3.10 abyss 2.3.10 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1042 1042 5543 5543 413 414 1301 1305 299 299 2030 2030 1754 5263 8874 26626
+abyss abyss-pe Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 http://www.bcgsc.ca/platform/bioinfo/software/abyss 2.3.10 abyss 2.3.10 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1042 1042 5543 5543 413 414 1301 1305 299 299 2030 2030 1754 5263 8874 26626
adapter_removal adapter_removal Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. 2022-05-04 https://github.com/MikkelSchubert/adapterremoval 2.3.4 adapterremoval 2.3.4 Up-to-date Fasta Manipulation, Sequence Analysis Sequence trimming, Sequence merging, Primer removal Sequence trimming, Sequence merging, Primer removal iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 62 62 348 348 0 0 0 0 0 0 0 0 62 186 348 1044
-add_input_name_as_column addName Add input name as column on an existing tabular file 2020-03-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python To update Text Manipulation mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 227 246 76834 86002 312 395 20174 20953 2 2 11 11 541 1725 97019 301004
-aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers 2021-01-03 https://github.com/BrendelGroup/AEGeAn 0.16.0 aegean 0.16.0 Up-to-date Transcriptomics, Sequence Analysis Sequence annotation Sequence annotation Sequence analysis, Gene structure Sequence analysis, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean gaeval GAEVAL Gene Annotation EVAluation. 1 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 77 77 200 200 39 39 83 83 44 44 1747 1747 160 480 2030 6090
+add_input_name_as_column addName Add input name as column on an existing tabular file 2020-03-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.2.0 python To update Text Manipulation mvdbeek https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 227 246 76834 86002 312 395 20174 20953 2 2 11 11 541 1725 97019 301004
+aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval AEGeAn toolkit wrappers 2021-01-03 https://github.com/BrendelGroup/AEGeAn 0.16.0 aegean 0.16.0 Up-to-date Transcriptomics, Sequence Analysis Sequence annotation Sequence annotation Sequence analysis, Gene structure Sequence analysis, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean gaeval GAEVAL Gene Annotation EVAluation. 1 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 77 77 200 200 39 39 83 83 44 44 1747 1747 160 480 2030 6090
aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.34.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 aldex2 ALDEx2 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 262 262 0 0 0 0 0 0 0 0 36 108 262 786
-allegro allegro Linkage and haplotype analysis from deCODE 2017-11-19 http://www.decode.com/software/ @VER@.0 allegro 3 To update Variant Analysis Sequence motif discovery Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Sequence analysis, Transcription factors and regulatory sites, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+allegro allegro Linkage and haplotype analysis from deCODE 2017-11-19 http://www.decode.com/software/ @VER@.0 allegro 3 To update Variant Analysis Sequence motif discovery Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Sequence analysis, Transcription factors and regulatory sites, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
amplican amplican AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.24.0 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican amplican amplican 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17 17 81 81 0 0 0 0 0 0 0 0 17 51 81 243
ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn ampvis2 2022-04-04 https://github.com/MadsAlbertsen/ampvis2/ 2.8.9 To update Metagenomics Analysis, Visualisation Analysis, Visualisation Biodiversity Biodiversity iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. 1 0 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 155 155 1213 1213 0 0 0 0 0 0 0 0 155 465 1213 3639
-ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.4.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc ancombc ANCOMBC 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 26 26 0 0 0 0 0 0 0 0 7 21 26 78
+ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.8.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc ancombc ANCOMBC 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 26 26 0 0 0 0 0 0 0 0 7 21 26 78
anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom Import, Export, Inspect and Manipulate Anndata and Loom objects 2019-03-21 https://anndata.readthedocs.io 0.10.9 anndata 0.6.22.post1 To update Single Cell, Spatial Omics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata anndata anndata "From https://anndata.readthedocs.io/en/latest/""Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray.""" 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 1826 1827 43047 43139 878 878 17240 17240 298 298 9309 9309 3002 9007 69596 208880
-annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages 2017-11-17 https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Up-to-date Genome annotation Annotation Annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2849 2973 29266 30655 5917 6355 59299 66180 1049 1049 5644 5644 9815 30007 94209 290897
-argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database 2024-08-28 https://github.com/BigDataBiology/argNorm 0.6.0 argnorm 0.6.0 Up-to-date Genome annotation Gene functional annotation Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+annotatemyids annotatemyids annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages 2017-11-17 https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids 3.18.0 bioconductor-org.hs.eg.db 3.18.0 Up-to-date Genome annotation Annotation Annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2849 2973 29266 30655 5917 6355 59299 66180 1049 1049 5644 5644 9815 30007 94209 290897
+argnorm argnorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database 2024-08-28 https://github.com/BigDataBiology/argNorm 0.6.0 argnorm 0.6.0 Up-to-date Genome annotation Gene functional annotation Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
arriba arriba, arriba_draw_fusions, arriba_get_filters Arriba detects fusion genes in RNA-Seq data after running RNA-STAR 2022-07-27 https://github.com/suhrig/arriba 2.4.0 arriba 2.4.0 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 71 71 3670 3670 2 2 3 3 10 10 234 234 83 249 3907 11721
-art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data 2015-02-11 http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 2014.11.03.0 art 2016.06.05 To update Sequence Analysis, Data Source Conversion Conversion Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 140 140 0 0 0 0 0 0 0 0 9 27 140 420
-assembly_stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 2023-06-21 https://github.com/rjchallis/assembly-stats 17.02 rjchallis-assembly-stats 17.02 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+art art_454, art_illumina, art_solid Simulator for Illumina, 454, and SOLiD sequencing data 2015-02-11 http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 2014.11.03.0 art 2016.06.05 To update Sequence Analysis, Data Source Conversion Conversion Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/art https://github.com/galaxyproject/tools-iuc/tree/main/tools/art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 140 140 0 0 0 0 0 0 0 0 9 27 140 420
+assembly_stats assembly_stats Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 2023-06-21 https://github.com/rjchallis/assembly-stats 17.02 rjchallis-assembly-stats 17.02 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
astral astral Tool for estimating an unrooted species tree given a set of unrooted gene trees 2024-08-28 https://github.com/smirarab/ASTRAL 5.7.8 astral-tree 5.7.8 Up-to-date Phylogenetics iuc https://github.com/usegalaxy-be/galaxytools/tree/main/astral https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 5 5 151 151 5 15 151 453
-augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2017-10-05 http://bioinf.uni-greifswald.de/augustus/ 3.4.0 augustus 3.5.0 To update Sequence Analysis Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families Gene transcripts, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1826 1988 12890 13988 2633 2633 14901 14901 511 511 6187 6187 4970 15072 33978 103032
-bakta bakta """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.""" 2022-09-01 https://github.com/oschwengers/bakta 1.9.4 bakta 1.10.1 To update Sequence Analysis Genome annotation Genome annotation Genomics, Sequence analysis, Bioinformatics Genomics, Sequence analysis, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 534 534 11117 11117 1 1 19 19 167 167 9601 9601 702 2106 20737 62211
+augustus augustus, augustus_training AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2017-10-05 http://bioinf.uni-greifswald.de/augustus/ 3.4.0 augustus 3.5.0 To update Sequence Analysis Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families Gene transcripts, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1826 1988 12890 13988 2633 2633 14901 14901 511 511 6187 6187 4970 15072 33978 103032
+bakta bakta """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.""" 2022-09-01 https://github.com/oschwengers/bakta 1.9.4 bakta 1.10.2 To update Sequence Analysis Genome annotation Genome annotation Genomics, Sequence analysis, Bioinformatics Genomics, Sequence analysis, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 534 534 11117 11117 1 1 19 19 167 167 9601 9601 702 2106 20737 62211
bam2fastx bam2fastx Convert PacBio Bam File to fasta or fastq file 2024-03-11 https://github.com/PacificBiosciences/pbtk 3.4.0 pbtk 3.4.0 Up-to-date Convert Formats, Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22 58 58 19 19 109 109 0 0 0 0 41 123 167 501
bam_to_scidx bam_to_scidx Contains a tool that converts a BAM file to an ScIdx file. 2015-12-07 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx 1.0.1 openjdk To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 20 83 131 50 210 329 785 0 0 0 0 65 360 412 1740
-bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 653 721 14693 15620 1656 5678 61872 101400 3 3 39 39 2312 11026 76604 270267
-bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2994 3180 115954 124795 6712 10660 95433 142254 497 497 5793 5793 10203 34743 217180 707202
+bamtools bamtools Operate on and transform BAM datasets in various ways using bamtools 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 653 721 14693 15620 1656 5678 61872 101400 3 3 39 39 2312 11026 76604 270267
+bamtools_filter bamFilter Filter BAM datasets on various attributes using bamtools filter 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2994 3180 115954 124795 6712 10660 95433 142254 497 497 5793 5793 10203 34743 217180 707202
bamutil bamutil_clip_overlap, bamutil_diff bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. 2021-03-29 https://github.com/statgen/bamUtil bamutil 1.0.15 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 45 45 21 21 69 69 1 1 258 258 42 126 372 1116
-bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily 2018-09-06 https://github.com/rrwick/Bandage 2022.09 bandage_ng 2022.09 Up-to-date Visualization Sequence assembly visualisation Sequence assembly visualisation Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage bandage Bandage 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. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 4951 5035 55392 56095 4916 4916 47603 47603 3121 3121 18089 18089 12988 39048 121084 363955
+bandage bandage_image, bandage_info Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily 2018-09-06 https://github.com/rrwick/Bandage 2022.09 bandage_ng 2022.09 Up-to-date Visualization Sequence assembly visualisation Sequence assembly visualisation Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage bandage Bandage 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. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 4951 5035 55392 56095 4916 4916 47603 47603 3121 3121 18089 18089 12988 39048 121084 363955
barcode_splitter barcode_splitter A utility to split sequence files using multiple sets of barcodes 2019-02-21 https://bitbucket.org/princeton_genomics/barcode_splitter/ 0.18.4.0 barcode_splitter 0.18.6 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 2023-09-06 https://github.com/lldelisle/baredSC 1.1.3 baredsc 1.1.3 Up-to-date Single Cell, Transcriptomics, Visualization Data retrieval, Expression correlation analysis, Differential gene expression profiling Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 8 8 111 111 10 10 29 29 4 4 21 21 22 66 161 483
-barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. 2017-08-25 https://github.com/tseemann/barrnap 1.2.2 barrnap 0.9 To update Sequence Analysis Gene prediction Gene prediction Genomics, Model organisms, Model organisms Genomics, Model organisms, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 316 316 6041 6041 0 0 0 0 240 322 6723 7273 556 1750 12764 38842
-basil basil Breakpoint detection, including large insertions 2019-05-22 https://github.com/seqan/anise_basil 1.2.0 anise_basil 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 82 83 306 311 99 99 467 467 0 0 0 0 181 544 773 2324
+barrnap barrnap Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. 2017-08-25 https://github.com/tseemann/barrnap 1.2.2 barrnap 0.9 To update Sequence Analysis Gene prediction Gene prediction Genomics, Model organisms, Model organisms Genomics, Model organisms, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 316 316 6041 6041 0 0 0 0 240 322 6723 7273 556 1750 12764 38842
+basil basil Breakpoint detection, including large insertions 2019-05-22 https://github.com/seqan/anise_basil 1.2.0 anise_basil 1.2.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 82 83 306 311 99 99 467 467 0 0 0 0 181 544 773 2324
bax2bam bax2bam BAX to BAM converter 2019-10-12 https://github.com/pacificbiosciences/bax2bam/ 0.0.11 bax2bam 0.0.11 Up-to-date Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 26 26 208 208 30 30 210 210 0 0 0 0 56 168 418 1254
bayescan BayeScan Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.0.1 To update Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan bayescan BayeScan 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 28 90 90 0 0 0 0 0 0 0 0 28 84 90 270
bbgbigwig bbgtobigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. 2024-06-14 https://www.encodeproject.org/software/bedgraphtobigwig/ 0.1 ucsc-bedgraphtobigwig 472 To update Convert Formats Sequence analysis Sequence analysis iuc https://www.encodeproject.org/software/bedgraphtobigwig/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 42 42 26 26 175 175 0 0 0 0 33 99 217 651
-bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole 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. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.13 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools bbmap BBMap 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. 6 3 5 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 768 768 11989 11989 652 652 4458 4458 80 80 2507 2507 1500 4500 18954 56862
+bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole 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. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.13 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools bbmap BBMap 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. 6 3 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 768 768 11989 11989 652 652 4458 4458 80 80 2507 2507 1500 4500 18954 56862
beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). 2023-08-11 https://github.com/EGA-archive/beacon2-ri-tools/tree/main 2.0.0 beacon2-ri-tools 2.0.0 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 9 9 33 33 0 0 0 0 0 0 0 0 9 27 33 99
-beagle beagle Beagle is a program for phasing and imputing missing genotypes. 2021-07-03 https://faculty.washington.edu/browning/beagle/beagle.html 5.2_21Apr21.304 beagle 5.4_22Jul22.46e To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 28 28 88 88 0 0 0 0 0 0 0 0 28 84 88 264
+beagle beagle Beagle is a program for phasing and imputing missing genotypes. 2021-07-03 https://faculty.washington.edu/browning/beagle/beagle.html 5.2_21Apr21.304 beagle 5.4_22Jul22.46e To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 28 28 88 88 0 0 0 0 0 0 0 0 28 84 88 264
bedops_sortbed bedops-sort-bed BEDOPS: high-performance genomic feature operations 2023-08-08 https://bedops.readthedocs.io/en/latest/ 2.4.41 bedops 2.4.41 Up-to-date Genomic Interval Operations iuc https://bedops.readthedocs.io/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 36 36 93 93 62 62 181 181 0 0 0 0 98 294 274 822
-bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic 2014-09-13 https://github.com/arq5x/bedtools2 2.31.1 bedtools 2.31.1 Up-to-date Genomic Interval Operations, Text Manipulation Mapping Mapping Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. 37 37 37 37 0 0 0 0 0 0 0 0 0 0 37 6 37 0 0 0 0 0 0 37 0 0 0 0 0 0 37 37 37 0 13235 14525 916111 962278 25849 41751 407944 647621 2486 2832 84008 89233 41570 142248 1408063 4515258
+bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bedtools is a powerful toolset for genome arithmetic 2014-09-13 https://github.com/arq5x/bedtools2 2.31.1 bedtools 2.31.1 Up-to-date Genomic Interval Operations, Text Manipulation Mapping Mapping Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. 37 37 37 0 0 0 0 0 0 0 0 0 0 0 0 37 6 37 0 0 0 0 0 37 0 0 0 0 0 0 37 37 37 0 13235 14525 916111 962278 25849 41751 407944 647621 2486 2832 84008 89233 41570 142248 1408063 4515258
bellerophon bellerophon Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. 2021-05-28 https://github.com/davebx/bellerophon 1.0 bellerophon 1.0 Up-to-date Sequence Analysis iuc https://github.com/davebx/bellerophon https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 1611 1611 67 67 763 763 30 30 543 543 359 1077 2917 8751
berokka berokka Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. 2019-03-08 https://github.com/tseemann/berokka 0.2.3 berokka 0.2.3 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 63 617 617 63 189 617 1851
bigscape bigscape Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE 1.1.9 bigscape 1.1.9 Up-to-date Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape BiG-SCAPE BiG-SCAPE 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 20 544 544 0 0 0 0 0 0 0 0 20 60 544 1632
bigwig_outlier_bed bigwig_outlier_bed pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files 2024-07-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed 0.2.2 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 218 218 0 0 0 0 0 0 0 0 5 15 218 654
-binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 126 126 0 0 0 0 0 0 0 0 42 126 126 378
+binning_refiner bin_refiner Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 42 42 126 126 0 0 0 0 0 0 0 0 42 126 126 378
bio_hansel bio_hansel Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel Biohansel BioHansel 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 32 33 349 359 53 53 364 364 0 0 0 0 85 256 713 2149
bioinformatics_cafe fasta_regex_finder Miscellanea of scripts for bioinformatics 2023-01-25 https://github.com/dariober/bioinformatics-cafe/ 0.1.0 python To update Sequence Analysis mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 97 97 1137 1137 71 71 1029 1029 0 0 0 0 168 504 2166 6498
biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis biotradis biotradis 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. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 375 375 6243 6243 0 0 0 0 375 1125 6243 18729
biscot biscot Bionano scaffolding correction tool 2023-01-06 https://github.com/institut-de-genomique/biscot 2.3.3 biscot 2.3.3 Up-to-date Assembly iuc https://github.com/bgruening/iuc/tree/master/tools/biscot https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 3 3 0 0 0 0 0 0 0 0 1 3 3 9
blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 BlastXML to gapped GFF3 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 102 102 585 585 63 63 172 172 16 16 135 135 181 543 892 2676
-bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment 2017-05-08 http://bowtie-bio.sourceforge.net/bowtie2 2.5.3 bowtie2 2.5.4 To update Next Gen Mappers Read mapping Read mapping Mapping, Genomics, Mapping Mapping, Genomics, Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 12133 13176 397893 427447 33086 52020 577209 903193 3779 4271 60105 67495 48998 167463 1035207 3468549
-bp_genbank2gff3 bp_genbank2gff3 Converts GenBank format files to GFF3 2015-08-14 https://bioperl.org/ 1.1 perl-bioperl 1.7.8 To update Sequence Analysis Data handling, Service invocation Data handling, Service invocation Genomics, Software engineering, Data management Genomics, Software engineering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 478 508 7738 7931 849 849 8301 8301 154 154 1369 1369 1481 4473 17408 52417
-bracken est_abundance Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://ccb.jhu.edu/software/bracken/ 3.0 bracken 3.0 Up-to-date Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 775 775 51378 51378 160 160 3298 3298 63 63 1660 1660 998 2994 56336 169008
-breseq breseq Predicts mutations in microbial genomes 2019-10-21 https://github.com/barricklab/breseq 0.35.5 breseq 0.39.0 To update Variant Analysis Polymorphism detection Polymorphism detection Sequencing, Sequence analysis, DNA mutation Sequencing, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq breseq breseq Runs Breseq software on a set of fastq files. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 98 98 2976 2976 0 0 0 0 70 70 884 884 168 504 3860 11580
+bowtie2 bowtie2 Bowtie2: Fast and sensitive read alignment 2017-05-08 http://bowtie-bio.sourceforge.net/bowtie2 2.5.3 bowtie2 2.5.4 To update Next Gen Mappers Read mapping Read mapping Mapping, Genomics, Mapping Mapping, Genomics, Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 12133 13176 397893 427447 33086 52020 577209 903193 3779 4271 60105 67495 48998 167463 1035207 3468549
+bp_genbank2gff3 bp_genbank2gff3 Converts GenBank format files to GFF3 2015-08-14 https://bioperl.org/ 1.1 perl-bioperl 1.7.8 To update Sequence Analysis Data handling, Service invocation Data handling, Service invocation Genomics, Software engineering, Data management Genomics, Software engineering iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 478 508 7738 7931 849 849 8301 8301 154 154 1369 1369 1481 4473 17408 52417
+bracken est_abundance Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://ccb.jhu.edu/software/bracken/ 3.0 bracken 3.0 Up-to-date Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 775 775 51378 51378 160 160 3298 3298 63 63 1660 1660 998 2994 56336 169008
+breseq breseq Predicts mutations in microbial genomes 2019-10-21 https://github.com/barricklab/breseq 0.35.5 breseq 0.39.0 To update Variant Analysis Polymorphism detection Polymorphism detection Sequencing, Sequence analysis, DNA mutation Sequencing, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq breseq breseq Runs Breseq software on a set of fastq files. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 98 98 2976 2976 0 0 0 0 70 70 884 884 168 504 3860 11580
brew3r_r brew3r_r Extend 3' end of a GTF using another GTF as a template 2024-06-11 https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html 1.0.2 To update Transcriptomics, RNA Genome annotation Genome annotation Transcriptomics, Genomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 2 2 6 6 0 0 0 0 3 9 7 21
-busco busco BUSCO assess genome and annotation completeness 2017-01-12 https://gitlab.com/ezlab/busco/-/releases 5.8.0 busco 5.8.2 To update Sequence Analysis Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco busco BUSCO 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3877 3926 102717 103051 3506 3506 34251 34251 2439 2525 33192 34369 9822 29601 170160 511991
-bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse 2017-11-21 http://bio-bwa.sourceforge.net/ 0.7.18 bwa 0.7.18 Up-to-date Next Gen Mappers Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 2 13526 14401 976935 1017671 32627 47624 474702 681286 4219 4954 79802 87191 50372 167723 1531439 4849026
-bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 2021-10-08 https://github.com/bwa-mem2/bwa-mem2 2.2.1 bwa-mem2 2.2.1 Up-to-date Next Gen Mappers Sequence alignment Sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 2324 2324 56619 56619 2808 2808 36631 36631 713 713 18121 18121 5845 17535 111371 334113
+busco busco BUSCO assess genome and annotation completeness 2017-01-12 https://gitlab.com/ezlab/busco/-/releases 5.8.0 busco 5.8.2 To update Sequence Analysis Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco busco BUSCO 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3877 3926 102717 103051 3506 3506 34251 34251 2439 2525 33192 34369 9822 29601 170160 511991
+bwa bwa_mem, bwa Wrapper for bwa mem, aln, sampe, and samse 2017-11-21 http://bio-bwa.sourceforge.net/ 0.7.18 bwa 0.7.18 Up-to-date Next Gen Mappers Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 2 13526 14401 976935 1017671 32627 47624 474702 681286 4219 4954 79802 87191 50372 167723 1531439 4849026
+bwa_mem2 bwa_mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 2021-10-08 https://github.com/bwa-mem2/bwa-mem2 2.2.1 bwa-mem2 2.2.1 Up-to-date Next Gen Mappers Sequence alignment Sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 2324 2324 56619 56619 2808 2808 36631 36631 713 713 18121 18121 5845 17535 111371 334113
bwameth bwameth Fast and accurate alignment of BS-seq reads 2016-09-14 https://github.com/brentp/bwa-meth 0.2.7 bwameth 0.2.7 Up-to-date Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 643 826 7970 11724 611 611 5524 5524 114 114 1242 1242 1368 4287 14736 47962
-cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program 2022-01-28 https://github.com/ComparativeGenomicsToolkit/cactus 2.7.1 To update Sequence Analysis Multiple sequence alignment, Genome alignment Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Genomics, Sequence assembly, Mapping, Phylogenetics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. 0 2 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 61 61 299 299 0 0 0 0 95 95 1339 1339 156 468 1638 4914
+cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program 2022-01-28 https://github.com/ComparativeGenomicsToolkit/cactus 2.7.1 To update Sequence Analysis Multiple sequence alignment, Genome alignment Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Genomics, Sequence assembly, Mapping, Phylogenetics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 61 61 299 299 0 0 0 0 95 95 1339 1339 156 468 1638 4914
calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. 2019-08-26 https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold 1.0.0 numpy To update Visualization, Genomic Interval Operations, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. 2021-05-04 0.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 1393 1393 0 0 0 0 0 0 0 0 10 30 1393 4179
cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 195 195 0 0 0 0 0 0 0 0 4 12 195 585
-cd_hit cd_hit Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 510 510 10414 10414 1 1 2 2 1 1 2 2 512 1536 10418 31254
+cd_hit cd_hit Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 510 510 10414 10414 1 1 2 2 1 1 2 2 512 1536 10418 31254
cemitool cemitool Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.26.0 bioconductor-cemitool 1.26.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool cemitool CEMiTool 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 225 225 61 61 271 271 0 0 0 0 93 279 496 1488
charts charts Enables advanced visualization options in Galaxy Charts 2018-01-30 https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1576 1822 3383 4001 3823 6880 7870 13727 108 145 249 350 5507 19861 11502 41082
-checkm 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 Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.3 checkm-genome 1.2.3 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 10 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 930 930 7500 7500 0 0 0 0 0 0 0 0 930 2790 7500 22500
+checkm 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 Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.3 checkm-genome 1.2.3 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 930 930 7500 7500 0 0 0 0 0 0 0 0 930 2790 7500 22500
chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema BSR-Based Allele Calling Algorithm 2024-04-13 https://github.com/B-UMMI/chewBBACA/tree/master chewbbaca 3.3.10 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 76 76 727 727 0 0 0 0 0 0 0 0 76 228 727 2181
chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify Chimeric Read Annotator for RNA-RNA interactome data 2020-01-19 https://github.com/pavanvidem/chira 1.4.3 chira 1.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 287 287 16542 16542 102 102 1061 1061 5 5 27 27 394 1182 17630 52890
chopin2 chopin2 Domain-Agnostic Supervised Learning with Hyperdimensional Computing 2023-01-18 https://github.com/cumbof/chopin2 1.0.9.post1 chopin2 To update Machine Learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 14 14 0 0 0 0 6 18 14 42
-chromeister chromeister ultra-fast pairwise genome comparisons 2020-09-30 https://github.com/estebanpw/chromeister 1.5.a chromeister 1.5.a Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 398 398 2696 2696 0 0 0 0 186 186 1235 1235 584 1752 3931 11793
+chromeister chromeister ultra-fast pairwise genome comparisons 2020-09-30 https://github.com/estebanpw/chromeister 1.5.a chromeister 1.5.a Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 398 398 2696 2696 0 0 0 0 186 186 1235 1235 584 1752 3931 11793
circexplorer2 circexplorer2 Comprehensive and integrative circular RNA analysis toolset. 2022-08-26 https://github.com/YangLab/CIRCexplorer2 2.3.8 circexplorer2 2.3.8 Up-to-date RNA, Assembly RNA splicing, Gene transcripts, Literature and language RNA splicing, Gene transcripts, Literature and language iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 524 524 0 0 0 0 0 0 0 0 32 96 524 1572
-circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy 2017-08-07 http://circos.ca/ 0.69.8 circos 0.69.9 To update Graphics Sequence visualisation Sequence visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. 11 11 11 11 0 0 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 2483 2483 26265 26265 3535 3535 31332 31332 999 999 26359 26359 7017 21051 83956 251868
+circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile Build Circos Plots in Galaxy 2017-08-07 http://circos.ca/ 0.69.8 circos 0.69.9 To update Graphics Sequence visualisation Sequence visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. 11 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 0 0 0 0 0 11 0 0 0 0 0 0 11 11 11 0 2483 2483 26265 26265 3535 3535 31332 31332 999 999 26359 26359 7017 21051 83956 251868
cite_seq_count cite_seq_count Count CMO/HTO 2023-01-18 https://github.com/Hoohm/CITE-seq-Count 1.4.4 cite-seq-count 1.4.5 To update Single Cell, Transcriptomics, Proteomics RNA-Seq quantification RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Transcriptomics, Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 21 21 5 5 9 9 1 1 18 18 10 30 48 144
-clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 1.0.8 clair3 1.0.10 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 clair3 Clair3 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 187 187 3388 3388 1 1 1 1 1 1 1 1 189 567 3390 10170
-clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1675 1785 79867 80817 3703 7380 49493 87884 670 728 8797 9713 6048 21989 138157 454728
+clair3 clair3 Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 1.0.8 clair3 1.0.10 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 clair3 Clair3 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 187 187 3388 3388 1 1 1 1 1 1 1 1 189 567 3390 10170
+clustalw clustalw ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1675 1785 79867 80817 3703 7380 49493 87884 670 728 8797 9713 6048 21989 138157 454728
clustering_from_distmat clustering_from_distmat Distance matrix-based hierarchical clustering using SciPy 2024-08-08 https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ 1.1.1 python To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 12 12 0 0 0 0 0 0 0 0 5 15 12 36
cnv-vcf2json cnv_vcf2json cnv-vcf2json Converts structural variants VCF file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 1.1.0 cnv-vcf2json To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 9 9 0 0 0 0 0 0 0 0 5 15 9 27
cnv_phenopacket cnv_phenopacket cnv-phenopacket Converts TSV metadata file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 1.0.2 cnv-phenopacket To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 6 2 6
@@ -623,355 +623,357 @@ cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_br
codeml codeml Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.7 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 64 65 61197 61220 0 0 0 0 0 0 0 0 64 193 61197 183614
cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac cojac COJAC 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. 2 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 22 22 2758 2758 10 10 20 20 0 0 0 0 32 96 2778 8334
colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 2024-03-24 https://github.com/sokrypton/ColabFold 1.5.5 To update Proteomics, Graphics Database search, Protein structure prediction, Fold recognition Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 6771 6771 0 0 0 0 50 150 6771 20313
-colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 2017-10-02 https://colibread.inria.fr/ 24.7.14 commet 24.7.14 Up-to-date Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 40 273 273 0 0 0 0 0 0 0 0 40 120 273 819
-collection_column_join collection_column_join Column Join on Collections 2016-05-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3827 4011 23979 25337 4645 5045 21671 25163 688 701 2939 3036 9160 28077 48589 150714
-collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection 2018-06-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers 0.0.2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1620 1630 6905 7102 1897 1897 7761 7761 243 243 1157 1157 3760 11290 15823 47666
-column_maker Add_a_column1 Compute an expression on every row 2019-06-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5422 6121 2940752 3907183 6095 13728 263254 737503 884 974 96478 97667 12401 45625 3300484 11343321
-column_order_header_sort column_order_header_sort Sort Column Order by heading 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 268 297 3735 3891 381 381 1923 1923 0 0 0 0 649 1976 5658 17130
-column_remove_by_header column_remove_by_header Remove columns by header 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 613 662 8331 8917 716 716 5206 5206 27 27 1976 1976 1356 4117 15513 47125
-compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.6 Up-to-date Sequence Analysis Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 39 266 266 15 15 28 28 0 0 0 0 54 162 294 882
-compose_text_param compose_text_param Compose a text parameter value using text, integer and float values 2019-05-09 0.1.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 689 691 45827 45831 303 303 7721 7721 121 121 1481 1481 1113 3341 55029 165091
+colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 2017-10-02 https://colibread.inria.fr/ 24.7.14 commet 24.7.14 Up-to-date Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 40 273 273 0 0 0 0 0 0 0 0 40 120 273 819
+collection_column_join collection_column_join Column Join on Collections 2016-05-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3827 4011 23979 25337 4645 5045 21671 25163 688 701 2939 3036 9160 28077 48589 150714
+collection_element_identifiers collection_element_identifiers Extract element identifiers of a collection 2018-06-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers 0.0.2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1620 1630 6905 7102 1897 1897 7761 7761 243 243 1157 1157 3760 11290 15823 47666
+column_maker Add_a_column1 Compute an expression on every row 2019-06-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5422 6121 2940752 3907183 6095 13728 263254 737503 884 974 96478 97667 12401 45625 3300484 11343321
+column_order_header_sort column_order_header_sort Sort Column Order by heading 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 268 297 3735 3891 381 381 1923 1923 0 0 0 0 649 1976 5658 17130
+column_remove_by_header column_remove_by_header Remove columns by header 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 613 662 8331 8917 716 716 5206 5206 27 27 1976 1976 1356 4117 15513 47125
+compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.6 Up-to-date Sequence Analysis Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 39 39 266 266 15 15 28 28 0 0 0 0 54 162 294 882
+compose_text_param compose_text_param Compose a text parameter value using text, integer and float values 2019-05-09 0.1.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 689 691 45827 45831 303 303 7721 7721 121 121 1481 1481 1113 3341 55029 165091
compress_file compress_file Compress files. 2022-02-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 290 290 6343 6343 286 286 3674 3674 59 59 11832 11832 635 1905 21849 65547
-concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering 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. 2022-02-18 https://github.com/BinPro/CONCOCT 1.1.0 concoct 1.1.0 Up-to-date Metagenomics Sequence clustering, Read binning Sequence clustering, Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 155 155 2105 2105 0 0 0 0 0 0 0 0 155 465 2105 6315
-contig_annotation_tool cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) 2019-11-27 https://github.com/dutilh/CAT 5.2.3 cat 6.0.1 To update Metagenomics Taxonomic classification, Sequence assembly, Coding region prediction Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat cat_bins CAT and BAT 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. 5 2 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 597 597 3835 3835 467 467 1359 1359 98 98 646 646 1162 3486 5840 17520
+concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering 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. 2022-02-18 https://github.com/BinPro/CONCOCT 1.1.0 concoct 1.1.0 Up-to-date Metagenomics Sequence clustering, Read binning Sequence clustering, Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 155 155 2105 2105 0 0 0 0 0 0 0 0 155 465 2105 6315
+contig_annotation_tool cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) 2019-11-27 https://github.com/dutilh/CAT 5.2.3 cat 6.0.1 To update Metagenomics Taxonomic classification, Sequence assembly, Coding region prediction Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat cat_bins CAT and BAT 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. 5 2 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 597 597 3835 3835 467 467 1359 1359 98 98 646 646 1162 3486 5840 17520
control_freec control_freec Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. 2020-07-22 http://boevalab.inf.ethz.ch/FREEC/ 11.6 gawk To update Variant Analysis Copy number estimation, Variant calling, Genome alignment Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining Oncology, Human genetics, Data mining iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 91 91 748 748 0 0 0 0 1 1 12 12 92 276 760 2280
cosg cosg Marker gene identification for single-cell sequencing data using COSG. 2024-05-29 https://github.com/genecell/COSG 1.0.1 cosg 1.0.1 Up-to-date Transcriptomics, Sequence Analysis, Single Cell Nucleic acid sequence analysis Nucleic acid sequence analysis Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg cosg COSG COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file 2017-10-16 https://github.com/galaxyproject/tools-iuc 0.0.4 perl-number-format 1.76 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-coverm coverm_contig, coverm_genome CoverM genome and contig wrappers 2022-04-26 https://github.com/wwood/CoverM 0.7.0 coverm 0.7.0 Up-to-date Sequence Analysis Local alignment Local alignment Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm coverm CoverM Read coverage calculator for metagenomics 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 151 151 1081 1081 0 0 0 0 0 0 0 0 151 453 1081 3243
+coverage_report CoverageReport2 Generate Detailed Coverage Report from BAM file 2017-10-16 https://github.com/galaxyproject/tools-iuc 0.0.4 perl-number-format 1.76 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+coverm coverm_contig, coverm_genome CoverM genome and contig wrappers 2022-04-26 https://github.com/wwood/CoverM 0.7.0 coverm 0.7.0 Up-to-date Sequence Analysis Local alignment Local alignment Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tools/coverm https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm coverm CoverM Read coverage calculator for metagenomics 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 151 151 1081 1081 0 0 0 0 0 0 0 0 151 453 1081 3243
crispr_studio crispr_studio CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. 2019-08-13 https://github.com/moineaulab/CRISPRStudio 1+galaxy0 crispr_studio 1 To update Sequence Analysis Visualisation Visualisation Sequence analysis, Genomics, Data visualisation Sequence analysis, Genomics, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 76 1052 1053 0 0 0 0 0 0 0 0 75 226 1052 3157
crosscontamination_barcode_filter crosscontamination_barcode_filter Barcode contamination discovery tool 2018-07-27 0.3 r-ggplot2 2.2.1 To update Transcriptomics, Visualization, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61 76 276 390 42 42 131 131 0 0 0 0 103 324 407 1335
crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig CrossMap converts genome coordinates or annotation files between genome assemblies 2016-04-04 http://crossmap.sourceforge.net/ 0.7.0 crossmap 0.7.0 Up-to-date Convert Formats, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap 5 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 5 6 5 0 331 331 2182 2182 903 903 5251 5251 0 0 0 0 1234 3702 7433 22299
-cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 171 300 768 1199 754 5750 2205 24981 46 98 251 493 971 8090 3224 33121
-cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 564 725 4176 6065 4952 20249 24284 117007 193 616 971 4231 5709 33008 29431 186165
-cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 870 1213 26122 33320 6984 27076 70653 349091 440 836 3963 10315 8294 45713 100738 594202
-cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 351 637 2406 3448 3641 13764 20978 67769 227 573 1209 3057 4219 23412 24593 123460
+cuffcompare cuffcompare Galaxy wrappers for the Cuffcompare tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 171 300 768 1199 754 5750 2205 24981 46 98 251 493 971 8090 3224 33121
+cuffdiff cuffdiff Galaxy wrappers for the Cuffdiff tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 564 725 4176 6065 4952 20249 24284 117007 193 616 971 4231 5709 33008 29431 186165
+cufflinks cufflinks Galaxy wrappers for the Cufflinks tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 870 1213 26122 33320 6984 27076 70653 349091 440 836 3963 10315 8294 45713 100738 594202
+cuffmerge cuffmerge Galaxy wrappers for the Cuffmerge tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 351 637 2406 3448 3641 13764 20978 67769 227 573 1209 3057 4219 23412 24593 123460
cuffnorm cuffnorm The Cuffnorm tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 81 114 374 701 273 1166 1032 13499 53 70 262 322 407 2164 1668 17858
cuffquant cuffquant The Cuffquant tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 54 71 408 732 267 1310 1964 15883 26 46 308 422 347 2121 2680 22397
-cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). 2018-02-20 https://cutadapt.readthedocs.org/en/stable/ 4.9 cutadapt 4.9 Up-to-date Fasta Manipulation, Fastq Manipulation, Sequence Analysis Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Genomics, Probes and primers, Sequencing lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11716 12601 259754 272370 18618 20162 334550 362356 3507 3627 64377 65986 33841 104072 658681 2018074
+cutadapt cutadapt Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). 2018-02-20 https://cutadapt.readthedocs.org/en/stable/ 4.9 cutadapt 5.0 To update Fasta Manipulation, Fastq Manipulation, Sequence Analysis Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Genomics, Probes and primers, Sequencing lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11716 12601 259754 272370 18618 20162 334550 362356 3507 3627 64377 65986 33841 104072 658681 2018074
cutesv cutesv Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. 2020-09-23 https://github.com/tjiangHIT/cuteSV 2.1.1 cutesv 2.1.1 Up-to-date Variant Analysis Split read mapping, Genotyping, Structural variation detection Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Sequencing, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 43 43 260 260 0 0 0 0 8 8 119 119 51 153 379 1137
cwpair2 cwpair2 Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. 2015-12-18 1.1.1 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 83 173 280 0 0 0 0 41 165 173 626
-dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers 2019-07-05 https://benjjneb.github.io/dada2/index.html bioconductor-dada2 1.30.0 To update Metagenomics Variant calling, DNA barcoding Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics Sequencing, Genetic variation, Microbial ecology, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 dada2 dada2 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. 10 10 11 10 0 0 0 0 0 0 0 0 0 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 2716 2716 92240 92240 5317 5317 179176 179176 394 394 12478 12478 8427 25281 283894 851682
-das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics 2022-06-23 https://github.com/cmks/DAS_Tool 1.1.7 das_tool 1.1.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool dastool dastool 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. 1 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 47 47 1323 1323 0 0 0 0 0 0 0 0 47 141 1323 3969
-data_manager_homer_preparse homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 2021-08-08 http://homer.ucsd.edu/homer/index.html 4.11 homer 4.11 Up-to-date Sequence Analysis Sequence motif discovery Sequence motif discovery iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 633 633 8531 8531 0 0 0 0 0 0 0 0 633 1899 8531 25593
+dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts DADA2 wrappers 2019-07-05 https://benjjneb.github.io/dada2/index.html bioconductor-dada2 1.30.0 To update Metagenomics Variant calling, DNA barcoding Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics Sequencing, Genetic variation, Microbial ecology, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 dada2 dada2 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. 10 10 11 0 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 10 0 2716 2716 92240 92240 5317 5317 179176 179176 394 394 12478 12478 8427 25281 283894 851682
+das_tool Fasta_to_Contig2Bin, das_tool DAS Tool for genome resolved metagenomics 2022-06-23 https://github.com/cmks/DAS_Tool 1.1.7 das_tool 1.1.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool dastool dastool 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. 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 47 47 1323 1323 0 0 0 0 0 0 0 0 47 141 1323 3969
+data_manager_homer_preparse homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 2021-08-08 http://homer.ucsd.edu/homer/index.html 4.11 homer 4.11 Up-to-date Sequence Analysis Sequence motif discovery Sequence motif discovery iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 633 633 8531 8531 0 0 0 0 0 0 0 0 633 1899 8531 25593
data_source_iris_tcga data_source_iris_tcga IRIS-TCGA Data source tool 2016-02-18 1.0.0 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-decontam decontam Removes decontamination features (ASVs/OTUs) using control samples 2024-09-13 https://github.com/benjjneb/decontam 1.22.0 bioconductor-decontam 1.22.0 Up-to-date Metagenomics Classification Classification Metagenomics, Microbial ecology, Sequencing Metagenomics, Microbial ecology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+decontam decontam Removes decontamination features (ASVs/OTUs) using control samples 2024-09-13 https://github.com/benjjneb/decontam 1.22.0 bioconductor-decontam 1.26.0 To update Metagenomics Classification Classification Metagenomics, Microbial ecology, Sequencing Metagenomics, Microbial ecology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
decontaminator decontaminator Deep Learning method for novel virus detection in sequencing data 2023-01-09 https://github.com/cbib/decontaminator 1.0.0 numpy To update Machine Learning Filtering Filtering Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 28 28 121 121 0 0 0 0 0 0 0 0 28 84 121 363
deepmicro deepmicro Representation learning and classification framework 2023-03-16 https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 Up-to-date Machine Learning Essential dynamics, Splitting, Community profiling Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics iuc https://github.com/paulzierep/DeepMicro https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 558 558 0 0 0 0 0 0 0 0 7 21 558 1674
-deepsig deepsig Predictor of signal peptides in proteins based on deep learning 2023-04-28 https://github.com/BolognaBiocomp/deepsig 1.2.5 deepsig 1.2.5 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 37 65 65 0 0 0 0 0 0 0 0 37 111 65 195
+deepsig deepsig Predictor of signal peptides in proteins based on deep learning 2023-04-28 https://github.com/BolognaBiocomp/deepsig 1.2.5 deepsig 1.2.5 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 37 65 65 0 0 0 0 0 0 0 0 37 111 65 195
deepvariant deepvariant DeepVariant is a deep learning-based variant caller 2021-09-06 https://github.com/google/deepvariant 1.5.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 325 325 2561 2561 460 460 2916 2916 0 0 0 0 785 2355 5477 16431
-deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables 2018-11-22 https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 To update Transcriptomics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4084 4155 22774 23146 5372 5372 33972 33972 846 846 4236 4236 10302 30977 60982 183318
-delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. 2020-09-28 https://github.com/dellytools/delly 0.9.1 delly 1.3.1 To update Variant Analysis Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis Indel detection, Structural variation detection, Genotyping DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 288 288 1451 1451 0 0 0 0 0 0 0 0 288 864 1451 4353
-deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution 2014-12-03 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 2.11.40.8 bioconductor-deseq2 1.42.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis, RNA-Seq analysis Differential gene expression analysis, RNA-Seq analysis RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 DESeq2 DESeq2 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11355 12514 97434 109474 24951 31957 183905 246475 2647 2905 18551 20166 38953 125282 299890 975895
-dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq 2015-09-25 https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html 1.48.0 bioconductor-dexseq 1.48.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Exonic splicing enhancer prediction Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 533 837 14874 16927 1403 2568 18475 28854 141 163 3854 4271 2077 7722 37203 124458
-diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.0.15 diamond 2.1.10 To update Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond diamond Diamond 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. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 3 3 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 3 3 0 1847 1895 61376 61746 1140 1556 23164 28729 522 522 63034 63034 3509 10991 147574 448657
-diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. 2018-01-21 http://bioconductor.org/packages/release/bioc/html/DiffBind.html 3.12.0 bioconductor-diffbind 3.12.0 Up-to-date ChIP-seq Differential binding analysis Differential binding analysis ChIP-seq ChIP-seq bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 606 652 7092 7663 1360 1916 14367 18624 69 84 1477 1640 2035 6722 22936 73799
-disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ disco 1.2 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco DISCO 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 124 139 358 406 384 384 1361 1361 0 0 0 0 508 1539 1719 5205
+deg_annotate deg_annotate Annotate DESeq2/DEXSeq output tables 2018-11-22 https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 To update Transcriptomics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 4084 4155 22774 23146 5372 5372 33972 33972 846 846 4236 4236 10302 30977 60982 183318
+delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. 2020-09-28 https://github.com/dellytools/delly 0.9.1 delly 1.3.1 To update Variant Analysis Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis Indel detection, Structural variation detection, Genotyping DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 6 0 0 0 0 0 0 6 6 0 0 288 288 1451 1451 0 0 0 0 0 0 0 0 288 864 1451 4353
+deseq2 deseq2 Differential gene expression analysis based on the negative binomial distribution 2014-12-03 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 2.11.40.8 bioconductor-deseq2 1.42.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis, RNA-Seq analysis Differential gene expression analysis, RNA-Seq analysis RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 DESeq2 DESeq2 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11355 12514 97434 109474 24951 31957 183905 246475 2647 2905 18551 20166 38953 125282 299890 975895
+dexseq dexseq, dexseq_count, plotdexseq Inference of differential exon usage in RNA-Seq 2015-09-25 https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html 1.48.0 bioconductor-dexseq 1.48.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Exonic splicing enhancer prediction Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 533 837 14874 16927 1403 2568 18475 28854 141 163 3854 4271 2077 7722 37203 124458
+diamond bg_diamond, bg_diamond_makedb, bg_diamond_view DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.0.15 diamond 2.1.10 To update Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond diamond Diamond 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. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 0 1 0 0 0 0 0 0 0 0 0 0 3 3 0 1847 1895 61376 61746 1140 1556 23164 28729 522 522 63034 63034 3509 10991 147574 448657
+diffbind diffbind Diffbind provides functions for processing ChIP-Seq data. 2018-01-21 http://bioconductor.org/packages/release/bioc/html/DiffBind.html 3.12.0 bioconductor-diffbind 3.12.0 Up-to-date ChIP-seq Differential binding analysis Differential binding analysis ChIP-seq ChIP-seq bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 606 652 7092 7663 1360 1916 14367 18624 69 84 1477 1640 2035 6722 22936 73799
+disco disco DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ disco 1.2 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco disco DISCO 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 124 139 358 406 384 384 1361 1361 0 0 0 0 508 1539 1719 5205
dnabot dnabot DNA assembly using BASIC on OpenTrons 2022-04-17 https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT 3.1.0 dnabot To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dnaweaver dnaweaver Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. 2022-12-08 https://github.com/Edinburgh-Genome-Foundry/DnaWeaver 1.0.2 dnaweaver_synbiocad 1.0.2 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 88 88 7358 7358 0 0 0 0 0 0 0 0 88 264 7358 22074
-drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.5.0 drep 3.5.0 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 113 113 916 916 0 0 0 0 0 0 0 0 113 339 916 2748
-dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data 2019-06-04 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html 1.10.0 bioconductor-dropletutils 1.22.0 To update Single Cell, Sequence Analysis Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics Sequencing, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils dropletutils 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 430 431 4413 4442 255 255 4403 4403 33 33 1816 1816 718 2155 10632 31925
+drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.5.0 drep 3.5.0 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 113 113 916 916 0 0 0 0 0 0 0 0 113 339 916 2748
+dropletutils dropletutils DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data 2019-06-04 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html 1.10.0 bioconductor-dropletutils 1.22.0 To update Single Cell, Sequence Analysis Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics Sequencing, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils dropletutils 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 430 431 4413 4442 255 255 4403 4403 33 33 1816 1816 718 2155 10632 31925
duplex_family_size_distribution fsd, fsd_beforevsafter, fsd_regions, td Tool that plots a histogram of sizes of read families 2019-10-24 1.0.2 matplotlib To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 578 578 0 0 0 0 34 102 578 1734
ebi_tools ebi_search_rest_results Tools to query and download data from several EMBL-EBI databases 2016-11-29 http://www.ebi.ac.uk/services/all 0.1.1 six To update Web Services, Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 133 163 276 406 547 547 1421 1421 0 0 0 0 680 2070 1697 5221
-edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline 2017-09-11 http://bioconductor.org/packages/release/bioc/html/edgeR.html 3.36.0 bioconductor-edger 4.0.16 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Genetics, RNA-Seq, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2423 2618 19294 20905 6341 7527 48876 58723 846 892 8010 8705 9610 30257 76180 240693
+edger edger Perform RNA-Seq differential expression analysis using edgeR pipeline 2017-09-11 http://bioconductor.org/packages/release/bioc/html/edgeR.html 3.36.0 bioconductor-edger 4.4.0 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Genetics, RNA-Seq, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2423 2618 19294 20905 6341 7527 48876 58723 846 892 8010 8705 9610 30257 76180 240693
ega_download_client pyega3 EGA python client uses the EGA REST API to download authorized datasets and files. 2020-09-02 https://github.com/EGA-archive/ega-download-client 5.0.2 pyega3 5.2.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 104 104 2716 2716 43 43 134 134 1 1 40 40 148 444 2890 8670
egsea egsea This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing 2017-12-28 https://bioconductor.org/packages/release/bioc/html/EGSEA.html 1.20.0 bioconductor-egsea 1.28.0 To update Transcriptomics, RNA, Statistics, Single Cell Gene set testing Gene set testing Systems biology Systems biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 371 402 2809 3060 759 759 5179 5179 226 226 1931 1931 1356 4099 9919 30008
-emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 107 107 107 107 0 0 0 0 0 0 0 0 0 0 0 0 107 0 0 0 0 0 0 107 0 0 0 0 0 0 107 107 107 0 4481 5039 143762 148864 13224 31140 151989 296028 2397 2705 24955 27001 20102 79088 320706 1113305
-ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 2020-06-10 https://github.com/usegalaxy-eu/ena-upload-cli 0.7.3 ena-upload-cli 0.7.4 To update Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 41 41 366 366 0 0 0 0 14 14 1302 1302 55 165 1668 5004
-enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API 2017-08-05 https://github.com/bebatut/enasearch enasearch 0.2.2 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 367 453 1989 2302 0 0 0 0 0 0 0 0 367 1187 1989 6280
+emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 107 107 107 0 0 0 0 0 0 0 0 0 0 0 0 0 0 107 0 0 0 0 0 107 0 0 0 0 0 0 107 107 107 0 4481 5039 143762 148864 13224 31140 151989 296028 2397 2705 24955 27001 20102 79088 320706 1113305
+ena_upload ena_upload Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 2020-06-10 https://github.com/usegalaxy-eu/ena-upload-cli 0.7.3 ena-upload-cli 0.7.4 To update Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 41 41 366 366 0 0 0 0 14 14 1302 1302 55 165 1668 5004
+enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data A Python library for interacting with ENA's API 2017-08-05 https://github.com/bebatut/enasearch enasearch 0.2.2 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 367 453 1989 2302 0 0 0 0 0 0 0 0 367 1187 1989 6280
ensembl_vep ensembl_vep Ensembl VEP: Annotate VCFs with variant effect predictions 2022-05-11 https://github.com/Ensembl/ensembl-vep 113.3 ensembl-vep 113.3 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 171 171 3051 3051 0 0 0 0 0 0 0 0 171 513 3051 9153
episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess EpiScanpy – Epigenomics single cell analysis in python 2023-03-13 https://github.com/colomemaria/epiScanpy 0.3.2 episcanpy 0.4.0 To update Single Cell, Epigenetics Enrichment analysis, Imputation Enrichment analysis, Imputation Epigenomics, Cell biology, DNA Epigenomics, Cell biology, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 80 80 880 880 37 37 221 221 3 3 49 49 120 360 1150 3450
+ete_treeviewer ete_treeviewer A toolkit for the analysis and visualization of trees. 2024-11-25 http://etetoolkit.org 3.1.3 curl To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit ete ete 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
evidencemodeler evidencemodeler EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. 2024-07-19 https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file 2.1.0 evidencemodeler 2.1.0 Up-to-date Genome annotation Gene prediction Gene prediction Gene expression, Gene structure Gene expression, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
exomedepth exomedepth ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data 2019-11-08 https://cran.r-project.org/package=ExomeDepth 1.1.0 r-exomedepth 1.1.16 To update Sequence Analysis, Variant Analysis Sequence analysis, Variant calling, Genotyping, Copy number estimation Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 61 61 517 517 184 184 2995 2995 0 0 0 0 245 735 3512 10536
-exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. 2018-08-02 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 exonerate 2.4.0 Up-to-date Sequence Analysis Pairwise sequence alignment, Protein threading, Genome alignment Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 188 1030 1072 189 189 1058 1058 35 35 922 922 409 1230 3010 9072
-export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview 0.20 export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan export2graphlan export2graphlan 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 580 607 5396 5938 168 168 628 628 107 107 519 519 855 2592 6543 20171
-extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 2016-01-14 3.0.3+galaxy3 bx-python 0.13.0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 1 0 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 813 923 9409 12735 2072 11791 20180 259099 20 63 168 611 2905 18587 29757 331959
+exonerate exonerate Exonerate is a generic tool for pairwise sequence comparison. 2018-08-02 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 exonerate 2.4.0 Up-to-date Sequence Analysis Pairwise sequence alignment, Protein threading, Genome alignment Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 188 1030 1072 189 189 1058 1058 35 35 922 922 409 1230 3010 9072
+export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview 0.20 export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan export2graphlan export2graphlan 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 580 607 5396 5938 168 168 628 628 107 107 519 519 855 2592 6543 20171
+extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 2016-01-14 3.0.3+galaxy3 bx-python 0.13.0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 813 923 9409 12735 2072 11791 20180 259099 20 63 168 611 2905 18587 29757 331959
falco falco A high throughput sequence QC analysis tool 2024-04-17 https://github.com/smithlabcode/falco/ 1.2.4 falco 1.2.4 Up-to-date Sequence Analysis Sequencing quality control, Visualisation, Read mapping Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Workflows, Mapping, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 34 4298 4298 0 0 0 0 0 0 0 0 34 102 4298 12894
-fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene fargene fARGene 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 128 601 601 232 232 1165 1165 0 0 0 0 360 1080 1766 5298
-fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 104 130 5191 5367 104 338 5191 15749
-fasta_formatter cshl_fasta_formatter FASTA Width formatter 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 237 288 5235 5486 480 2039 4060 25609 73 89 816 1093 790 3996 10111 52410
-fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 71 108 497 808 216 703 2249 5479 18 20 415 437 305 1441 3161 13046
+fargene fargene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene fargene fARGene 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 128 128 601 601 232 232 1165 1165 0 0 0 0 360 1080 1766 5298
+fasta_clipping_histogram cshl_fasta_clipping_histogram Length Distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 104 130 5191 5367 104 338 5191 15749
+fasta_formatter cshl_fasta_formatter FASTA Width formatter 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 237 288 5235 5486 480 2039 4060 25609 73 89 816 1093 790 3996 10111 52410
+fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 71 108 497 808 216 703 2249 5479 18 20 415 437 305 1441 3161 13046
fasta_nucleotide_color_plot fasta_nucleotide_color_plot Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. 2016-03-06 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot 1.0.1 openjdk To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 42 47 164 179 128 170 758 905 0 0 0 0 170 557 922 2928
-fasta_stats fasta-stats Display summary statistics for a fasta file. 2018-11-21 https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3104 3259 43726 44512 3693 3693 19941 19941 2467 2650 16788 18589 9264 28130 80455 243952
-fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani fastani FastANI 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. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 603 603 6685 6685 0 0 0 0 0 0 0 0 603 1809 6685 20055
+fasta_stats fasta-stats Display summary statistics for a fasta file. 2018-11-21 https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3104 3259 43726 44512 3693 3693 19941 19941 2467 2650 16788 18589 9264 28130 80455 243952
+fastani fastani Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani fastani FastANI 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. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 603 603 6685 6685 0 0 0 0 0 0 0 0 603 1809 6685 20055
fastk fastk_fastk FastK: A K-mer counter (for HQ assembly data sets) 2024-05-03 https://github.com/thegenemyers/FASTK 1.1.0 fastk 1.1.0 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 136 136 0 0 0 0 0 0 0 0 11 33 136 408
-fastp fastp Fast all-in-one preprocessing for FASTQ files 2018-03-07 https://github.com/OpenGene/fastp 0.24.0 fastp 0.24.0 Up-to-date Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp fastp fastp 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 6847 6909 1126086 1127111 10722 10722 422259 422259 2242 2242 76462 76462 19811 59495 1624807 4875446
-fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 215 240 8604 8799 919 2957 54200 75329 76 85 1562 1680 1210 5702 64366 214540
+fastp fastp Fast all-in-one preprocessing for FASTQ files 2018-03-07 https://github.com/OpenGene/fastp 0.24.0 fastp 0.24.0 Up-to-date Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp fastp fastp 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 6847 6909 1126086 1127111 10722 10722 422259 422259 2242 2242 76462 76462 19811 59495 1624807 4875446
+fastq_combiner fastq_combiner Combine FASTA and QUAL into FASTQ 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 215 240 8604 8799 919 2957 54200 75329 76 85 1562 1680 1210 5702 64366 214540
fastq_dl fastq_dl Download FASTQ files from ENA. 2024-11-14 https://github.com/rpetit3/fastq-dl 3.0.0 fastq-dl 3.0.0 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fastq_filter fastq_filter Filter FASTQ reads by quality score and length 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 690 771 15582 18350 2715 9239 40489 121585 214 287 4657 5793 3619 17535 60728 267184
-fastq_groomer fastq_groomer Convert between various FASTQ quality formats. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2576 2995 92594 102535 9437 44701 179461 897457 664 1073 15434 25533 12677 74123 287489 1600503
-fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 215 267 2488 3132 834 2121 6241 14508 131 158 4121 4592 1180 4906 12850 47932
-fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43 44 234 249 288 983 2648 8092 12 17 442 466 343 1730 3324 15455
-fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 532 657 5873 8936 1889 2366 14738 20229 225 261 2316 2711 2646 8576 22927 77730
-fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2348 2492 18216 19573 3482 3851 23484 25936 1402 1442 6207 6551 7232 22249 47907 147874
-fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 536 679 15628 17130 1954 5716 24157 58368 172 214 1941 2266 2662 11933 41726 161216
-fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 459 535 3169 3521 1410 3441 19309 30747 219 247 807 1023 2088 8399 23285 81861
-fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 131 176 1271 1393 2073 8850 12763 58819 32 51 430 479 2236 13549 14464 89619
-fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 44 47 335 352 269 2229 1583 9696 15 27 1131 1254 328 2959 3049 17400
-fastq_quality_filter cshl_fastq_quality_filter Filter by quality 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3826 4062 17279 18386 6055 12590 55268 136888 1854 2043 7685 9356 11735 42165 80232 325094
-fastq_stats fastq_stats FASTQ Summary Statistics by column 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 680 815 3858 4595 3159 14109 15213 81513 184 256 3855 4163 4023 23226 22926 136123
-fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1151 1234 36069 37805 2691 6370 45213 99852 408 609 8457 13335 4250 16713 89739 330470
-fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 269 297 12895 14110 612 1810 13315 30673 64 87 5125 5373 945 4084 31335 112826
-fastq_trimmer fastq_trimmer FASTQ Trimmer by quality 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 582 665 10114 11383 1986 8818 23906 92351 108 212 1588 2607 2676 15047 35608 177557
-fastqc fastqc Read QC reports using FastQC 2017-01-11 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 0.74+galaxy1 fastqc 0.12.1 To update Fastq Manipulation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Sequencing, Data quality management, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 0 41344 43940 1784056 1913280 90828 140008 2269843 3195869 14195 16026 410004 445555 146367 492708 4463903 14482510
-fastqe fastqe FASTQE 2020-07-13 https://fastqe.com/ 0.3.1+galaxy0 fastqe 0.3.3 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2350 2350 5162 5162 4714 4714 10176 10176 991 991 2610 2610 8055 24165 17948 53844
-fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3421 3732 208349 217568 5108 13227 131388 245005 679 679 18655 18655 9208 36054 358392 1198012
-fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ 2.1.10 fasttree 2.1.11 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1049 1071 65542 65631 2147 2147 25992 25992 649 745 6733 7339 3845 11653 98267 295496
-fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 88 101 1769 2020 358 2424 6948 24960 32 50 623 998 478 3531 9340 46658
-fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 225 260 16957 18124 919 2720 37001 89126 56 68 863 989 1200 5448 54821 217881
-fastx_clipper cshl_fastx_clipper Clip adapter sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 178 212 3140 3520 1198 6006 13975 117900 36 55 409 712 1412 9097 17524 157180
-fastx_collapser cshl_fastx_collapser Collapse sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 326 349 64187 67981 781 3067 87477 185555 58 78 16563 17125 1165 5824 168227 607115
-fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 61 92 174 272 1056 4180 4295 25068 70 89 1127 1171 1187 6735 5596 37703
-fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 168 206 2218 2344 3784 9866 20551 60032 234 256 2347 2460 4186 18700 25116 115068
-fastx_renamer cshl_fastx_renamer Rename sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 180 214 2364 2526 303 1024 6572 11745 49 64 462 696 532 2366 9398 33763
-fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 356 415 10707 12597 574 1527 21568 67304 61 78 719 861 991 4002 32994 146750
-fastx_trimmer cshl_fastx_trimmer Trim sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 550 641 13584 14557 2034 8390 123676 206733 229 267 2819 4757 2813 14924 140079 506205
-featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ 2.0.6 subread 2.0.6 Up-to-date RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts featurecounts FeatureCounts 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11699 12547 740719 770524 23272 27598 643892 784396 2348 2463 66108 68867 37319 117246 1450719 4525225
-feelnc feelnc Galaxy wrapper for FEELnc 2018-03-27 https://github.com/tderrien/FEELnc 0.2.1 feelnc 0.2 To update Sequence Analysis Annotation, Classification Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 95 99 1375 1500 116 116 797 797 3 3 59 59 214 646 2231 6818
+fastq_filter fastq_filter Filter FASTQ reads by quality score and length 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 690 771 15582 18350 2715 9239 40489 121585 214 287 4657 5793 3619 17535 60728 267184
+fastq_groomer fastq_groomer Convert between various FASTQ quality formats. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2576 2995 92594 102535 9437 44701 179461 897457 664 1073 15434 25533 12677 74123 287489 1600503
+fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 215 267 2488 3132 834 2121 6241 14508 131 158 4121 4592 1180 4906 12850 47932
+fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 43 44 234 249 288 983 2648 8092 12 17 442 466 343 1730 3324 15455
+fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 532 657 5873 8936 1889 2366 14738 20229 225 261 2316 2711 2646 8576 22927 77730
+fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2348 2492 18216 19573 3482 3851 23484 25936 1402 1442 6207 6551 7232 22249 47907 147874
+fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 536 679 15628 17130 1954 5716 24157 58368 172 214 1941 2266 2662 11933 41726 161216
+fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 459 535 3169 3521 1410 3441 19309 30747 219 247 807 1023 2088 8399 23285 81861
+fastq_quality_boxplot cshl_fastq_quality_boxplot Draw quality score boxplot 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 131 176 1271 1393 2073 8850 12763 58819 32 51 430 479 2236 13549 14464 89619
+fastq_quality_converter cshl_fastq_quality_converter Quality format converter (ASCII-Numeric) 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 44 47 335 352 269 2229 1583 9696 15 27 1131 1254 328 2959 3049 17400
+fastq_quality_filter cshl_fastq_quality_filter Filter by quality 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3826 4062 17279 18386 6055 12590 55268 136888 1854 2043 7685 9356 11735 42165 80232 325094
+fastq_stats fastq_stats FASTQ Summary Statistics by column 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 680 815 3858 4595 3159 14109 15213 81513 184 256 3855 4163 4023 23226 22926 136123
+fastq_to_fasta cshl_fastq_to_fasta FASTQ to FASTA converter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1151 1234 36069 37805 2691 6370 45213 99852 408 609 8457 13335 4250 16713 89739 330470
+fastq_to_tabular fastq_to_tabular FASTQ to Tabular converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 269 297 12895 14110 612 1810 13315 30673 64 87 5125 5373 945 4084 31335 112826
+fastq_trimmer fastq_trimmer FASTQ Trimmer by quality 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 582 665 10114 11383 1986 8818 23906 92351 108 212 1588 2607 2676 15047 35608 177557
+fastqc fastqc Read QC reports using FastQC 2017-01-11 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 0.74+galaxy1 fastqc 0.12.1 To update Fastq Manipulation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Sequencing, Data quality management, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 1 1 1 1 1 1 0 41344 43940 1784056 1913280 90828 140008 2269843 3195869 14195 16026 410004 445555 146367 492708 4463903 14482510
+fastqe fastqe FASTQE 2020-07-13 https://fastqe.com/ 0.3.1+galaxy0 fastqe 0.3.3 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2350 2350 5162 5162 4714 4714 10176 10176 991 991 2610 2610 8055 24165 17948 53844
+fastqtofasta fastq_to_fasta_python FASTQ to FASTA converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 3421 3732 208349 217568 5108 13227 131388 245005 679 679 18655 18655 9208 36054 358392 1198012
+fasttree fasttree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ 2.1.10 fasttree 2.1.11 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1049 1071 65542 65631 2147 2147 25992 25992 649 745 6733 7339 3845 11653 98267 295496
+fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 88 101 1769 2020 358 2424 6948 24960 32 50 623 998 478 3531 9340 46658
+fastx_barcode_splitter cshl_fastx_barcode_splitter Barcode Splitter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 225 260 16957 18124 919 2720 37001 89126 56 68 863 989 1200 5448 54821 217881
+fastx_clipper cshl_fastx_clipper Clip adapter sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 178 212 3140 3520 1198 6006 13975 117900 36 55 409 712 1412 9097 17524 157180
+fastx_collapser cshl_fastx_collapser Collapse sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 326 349 64187 67981 781 3067 87477 185555 58 78 16563 17125 1165 5824 168227 607115
+fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution Draw nucleotides distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 61 92 174 272 1056 4180 4295 25068 70 89 1127 1171 1187 6735 5596 37703
+fastx_quality_statistics cshl_fastx_quality_statistics Compute quality statistics 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 168 206 2218 2344 3784 9866 20551 60032 234 256 2347 2460 4186 18700 25116 115068
+fastx_renamer cshl_fastx_renamer Rename sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 180 214 2364 2526 303 1024 6572 11745 49 64 462 696 532 2366 9398 33763
+fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 356 415 10707 12597 574 1527 21568 67304 61 78 719 861 991 4002 32994 146750
+fastx_trimmer cshl_fastx_trimmer Trim sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 550 641 13584 14557 2034 8390 123676 206733 229 267 2819 4757 2813 14924 140079 506205
+featurecounts featurecounts featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ 2.0.6 subread 2.0.8 To update RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts featurecounts FeatureCounts 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 11699 12547 740719 770524 23272 27598 643892 784396 2348 2463 66108 68867 37319 117246 1450719 4525225
+feelnc feelnc Galaxy wrapper for FEELnc 2018-03-27 https://github.com/tderrien/FEELnc 0.2.1 feelnc 0.2 To update Sequence Analysis Annotation, Classification Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 95 99 1375 1500 116 116 797 797 3 3 59 59 214 646 2231 6818
fermikit fermi2, fermikit_variants FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. 2017-01-05 https://github.com/lh3/fermikit r193 fermi2 r193 Up-to-date Assembly, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fgsea fgsea Perform gene set testing using fgsea 2018-10-19 https://bioconductor.org/packages/release/bioc/html/fgsea.html 1.8.0+galaxy1 bioconductor-fgsea 1.28.0 To update Visualization, Transcriptomics, Statistics, Single Cell Gene-set enrichment analysis Gene-set enrichment analysis Genetics Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 582 607 5618 5820 938 938 21673 21673 110 110 869 869 1630 4915 28160 84682
-filtlong filtlong Filtlong - Filtering long reads by quality 2018-09-14 https://github.com/rrwick/Filtlong 0.2.1 filtlong 0.2.1 Up-to-date Fastq Manipulation, Sequence Analysis Filtering, Sequencing quality control Filtering, Sequencing quality control iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong filtlong Filtlong 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1575 53310 53944 726 726 25043 25043 593 593 10824 10824 2818 8530 89177 268165
+fgsea fgsea Perform gene set testing using fgsea 2018-10-19 https://bioconductor.org/packages/release/bioc/html/fgsea.html 1.8.0+galaxy1 bioconductor-fgsea 1.32.0 To update Visualization, Transcriptomics, Statistics, Single Cell Gene-set enrichment analysis Gene-set enrichment analysis Genetics Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 582 607 5618 5820 938 938 21673 21673 110 110 869 869 1630 4915 28160 84682
+filtlong filtlong Filtlong - Filtering long reads by quality 2018-09-14 https://github.com/rrwick/Filtlong 0.2.1 filtlong 0.2.1 Up-to-date Fastq Manipulation, Sequence Analysis Filtering, Sequencing quality control Filtering, Sequencing quality control iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong filtlong Filtlong 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1499 1575 53310 53944 726 726 25043 25043 593 593 10824 10824 2818 8530 89177 268165
flair flair_collapse, flair_correct FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. 2020-11-06 https://github.com/BrooksLabUCSC/flair 1.5 flair 2.0.0 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 41 41 1985 1985 0 0 0 0 0 0 0 0 41 123 1985 5955
-flash flash Fast Length Adjustment of SHort reads 2017-09-25 https://ccb.jhu.edu/software/FLASH/ 1.2.11 flash 1.2.11 Up-to-date Assembly, Fastq Manipulation Read pre-processing, Sequence merging, Sequence assembly Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 239 255 22017 22304 462 709 9399 14886 1 1 4 4 702 2369 31420 100034
-fraggenescan fraggenescan Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ fraggenescan 1.31 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 162 1257 1450 0 0 0 0 45 45 1052 1052 195 597 2309 7120
-freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool 2017-01-11 https://github.com/ekg/freebayes 1.3.8 freebayes 1.3.8 Up-to-date Variant Analysis Variant calling, Statistical calculation Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Genomics, Genetic variation, Rare diseases devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 8158 8794 149715 171093 15996 25107 144708 256315 2251 2571 19156 21936 26405 89282 313579 1076502
-freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 1.5.2 freyja 1.5.2 Up-to-date Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 101 101 21757 21757 21 21 217 217 0 0 0 0 122 366 21974 65922
-gatk4_mutect2 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK 2019-10-28 https://software.broadinstitute.org/gatk/gatk4 4.1.7.0 gatk4 4.6.1.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 452 452 3463 3463 1639 1639 9040 9040 0 0 0 0 2091 6273 12503 37509
-gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 2017-06-23 http://bioinf.iasi.cnr.it/gdcwebapp/ 1.0.0 python To update Data Source, Convert Formats iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-gecko gecko Ungapped genome comparison 2020-11-25 https://github.com/otorreno/gecko 1.2 gecko 1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 235 235 723 723 0 0 0 0 95 95 786 786 330 990 1509 4527
-gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation 2014-11-09 https://github.com/arq5x/gemini 0.20.1 gemini 0.30.2 To update Sequence Analysis, Next Gen Mappers Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini gemini GEMINI 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. 1 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1863 1992 4967 5475 279 370 992 1118 423 425 3756 3811 2565 7917 9715 29834
-genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals 2020-08-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1 1 1 1 0 1 0 0 0 1 0 0 0 1 1 1 0 1 0 0 0 0 1 1 0 0 0 0 1 1 1 1 1 0 2 2 4 4 23 279 221 2905 0 0 0 0 25 331 225 3359
+flash flash Fast Length Adjustment of SHort reads 2017-09-25 https://ccb.jhu.edu/software/FLASH/ 1.2.11 flash 1.2.11 Up-to-date Assembly, Fastq Manipulation Read pre-processing, Sequence merging, Sequence assembly Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 239 255 22017 22304 462 709 9399 14886 1 1 4 4 702 2369 31420 100034
+fraggenescan fraggenescan Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ fraggenescan 1.31 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 150 162 1257 1450 0 0 0 0 45 45 1052 1052 195 597 2309 7120
+freebayes freebayes, bamleftalign Galaxy Freebayes Bayesian genetic variant detector tool 2017-01-11 https://github.com/ekg/freebayes 1.3.8 freebayes 1.3.8 Up-to-date Variant Analysis Variant calling, Statistical calculation Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Genomics, Genetic variation, Rare diseases devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 8158 8794 149715 171093 15996 25107 144708 256315 2251 2571 19156 21936 26405 89282 313579 1076502
+freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 1.5.2 freyja 1.5.2 Up-to-date Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 101 101 21757 21757 21 21 217 217 0 0 0 0 122 366 21974 65922
+gatk4_mutect2 gatk4_mutect2 A Galaxy wrapper for Mutect2 from GATK 2019-10-28 https://software.broadinstitute.org/gatk/gatk4 4.1.7.0 gatk4 4.6.1.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 452 452 3463 3463 1639 1639 9040 9040 0 0 0 0 2091 6273 12503 37509
+gdcwebapp data_source_gdcwebapp GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 2017-06-23 http://bioinf.iasi.cnr.it/gdcwebapp/ 1.0.0 python To update Data Source, Convert Formats iuc https://github.com/fabio-cumbo/GDCWebApp4Galaxy https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+gecko gecko Ungapped genome comparison 2020-11-25 https://github.com/otorreno/gecko 1.2 gecko 1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 235 235 723 723 0 0 0 0 95 95 786 786 330 990 1509 4527
+gem_tools gem_check_memote, gem_escher_visualization, gem_extract_exchange, gem_flux_distribution, gem_flux_variability_analysis, gem_knockout, gem_phenotype_phase_plane Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. 2024-12-01 https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology 0.29.1 cobra 0.21.0 To update Metabolomics, Systems Biology, Synthetic Biology iuc https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ GEMINI: a flexible framework for exploring genome variation 2014-11-09 https://github.com/arq5x/gemini 0.20.1 gemini 0.30.2 To update Sequence Analysis, Next Gen Mappers Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini gemini GEMINI 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. 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1863 1992 4967 5475 279 370 992 1118 423 425 3756 3811 2565 7917 9715 29834
+genebed_maf_to_fasta GeneBed_Maf_Fasta2 Stitch gene blocks given a set of coding exon intervals 2020-08-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta 1 1 1 0 0 1 0 0 0 1 1 0 0 0 1 1 1 0 1 0 0 0 0 1 0 0 0 0 1 1 1 1 1 0 2 2 4 4 23 279 221 2905 0 0 0 0 25 331 225 3359
genehunter_modscore genehunter_modscore Maximised LOD score pedigree analysis utility 2017-11-27 https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 3.0.0 ghm 3.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
geneiobio gene_iobio_display_generation_iframe Gene.iobio is an interactive tool for variant and trio analysis. 2023-06-20 https://github.com/iobio/gene.iobio 4.7.1+galaxy1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 101 101 0 0 0 0 6 6 59 59 31 93 160 480
genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." 2015-12-18 numpy To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 104 197 445 660 0 0 0 0 104 405 445 1550
-genomescope genomescope Analyze unassembled short reads 2021-04-30 https://github.com/tbenavi1/genomescope2.0 2.0.1 genomescope2 2.0.1 Up-to-date Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 665 665 3181 3181 435 435 2112 2112 148 148 1622 1622 1248 3744 6915 20745
+genomescope genomescope Analyze unassembled short reads 2021-04-30 https://github.com/tbenavi1/genomescope2.0 2.0.1 genomescope2 2.0.1 Up-to-date Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 665 665 3181 3181 435 435 2112 2112 148 148 1622 1622 1248 3744 6915 20745
genomic_super_signature genomic_super_signature Interpretation of RNAseq experiments through robust, efficient comparison to public databases 2022-01-12 https://github.com/shbrief/GenomicSuperSignature 1.2.0 bioconductor-genomicsupersignature 1.10.0 To update Sequence Analysis, RNA, Transcriptomics Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 13 13 47 47 0 0 0 0 0 0 0 0 13 39 47 141
genrich genrich Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). 2019-07-05 https://github.com/jsh58/Genrich 0.5+galaxy2 genrich 0.6.1 To update ChIP-seq iuc https://github.com/jsh58/Genrich https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 402 405 3534 3577 419 419 2840 2840 31 31 571 571 852 2559 6945 20878
get_hrun get_hrun Annotate indel variants with homopolymer context 2021-03-02 https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.8.1.3 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 9 9 0 0 0 0 0 0 0 0 5 15 9 27
getorganelle get_annotated_regions_from_gb, get_organelle_from_reads GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. 2022-03-15 https://github.com/Kinggerm/GetOrganelle 1.7.7.1 getorganelle 1.7.7.1 Up-to-date Assembly De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 159 159 1542 1542 0 0 0 0 64 64 587 587 223 669 2129 6387
-gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format 2019-06-18 http://gfa-spec.github.io/GFA-spec/ 0.1.2 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 763 765 9664 9775 493 493 5623 5623 135 135 1000 1000 1391 4175 16287 48972
-gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 68 68 806 812 37 37 197 197 12 12 132 132 117 351 1135 3411
-gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. 2017-03-27 https://github.com/gpertea/gffcompare/ 0.12.6 gffcompare 0.12.6 Up-to-date Transcriptomics Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 916 999 3560 3980 1713 2521 5281 8000 208 225 1468 1642 2837 9419 10309 34240
-gffread gffread gffread filters and/or converts GFF3/GTF2 records 2019-10-29 http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ 0.12.7 gffread 0.12.7 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread gffread gffread program for filtering, converting and manipulating GFF files 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1740 1829 12828 13716 2588 3486 15217 23818 732 732 4423 4423 5060 16167 32468 106893
-ggplot2_heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package 2019-02-10 https://github.com/cran/gplots 3.2.0 r-gplots 2.17.0 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 4645 5114 46700 50808 5799 6830 64214 70429 704 724 7783 7912 11148 34964 118697 366543
+gfa_to_fa gfa_to_fa gfa_to_fa - Converting GFA format to Fasta format 2019-06-18 http://gfa-spec.github.io/GFA-spec/ 0.1.2 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 763 765 9664 9775 493 493 5623 5623 135 135 1000 1000 1391 4175 16287 48972
+gff3_rebase gff3.rebase Rebase a GFF against a parent GFF (e.g. an original genome) 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 68 68 806 812 37 37 197 197 12 12 132 132 117 351 1135 3411
+gffcompare gffcompare Galaxy wrappers for Geo Pertea's GffCompare package. 2017-03-27 https://github.com/gpertea/gffcompare/ 0.12.6 gffcompare 0.12.6 Up-to-date Transcriptomics Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 916 999 3560 3980 1713 2521 5281 8000 208 225 1468 1642 2837 9419 10309 34240
+gffread gffread gffread filters and/or converts GFF3/GTF2 records 2019-10-29 http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ 0.12.7 gffread 0.12.7 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread gffread gffread program for filtering, converting and manipulating GFF files 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1740 1829 12828 13716 2588 3486 15217 23818 732 732 4423 4423 5060 16167 32468 106893
+ggplot2_heatmap2 ggplot2_heatmap2 heatmap.2 function from the R gplots package 2019-02-10 https://github.com/cran/gplots 3.2.0 r-gplots 2.17.0 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 4645 5114 46700 50808 5799 6830 64214 70429 704 724 7783 7912 11148 34964 118697 366543
ggupset emc-ggupset Create Upset Plots with ggupset 2022-12-17 https://github.com/const-ae/ggupset 1.0 r-ggupset To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html 1.50.0 bioconductor-goseq 1.54.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2807 3139 20207 21960 3066 3321 24488 26198 545 545 4155 4155 6418 19841 48850 150013
+goseq goseq goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html 1.50.0 bioconductor-goseq 1.54.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 2807 3139 20207 21960 3066 3321 24488 26198 545 545 4155 4155 6418 19841 48850 150013
gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more 2019-10-30 https://biit.cs.ut.ee/gprofiler @TOOL_VERSION@+galaxy11 r-gprofiler2 To update Statistics, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 614 614 4001 4001 1238 1238 7882 7882 0 0 0 0 1852 5556 11883 35649
graphembed graphembed Compute a 2D embedding of a data matrix given supervised class information 2019-12-10 https://github.com/fabriziocosta/GraphEmbed 2.4 graph_embed 2.4 Up-to-date Statistics, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 6 78 78 43 43 120 120 0 0 0 0 49 147 198 594
-graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan GraPhlAn 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. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1285 1350 9816 10927 368 368 1273 1273 242 242 1104 1104 1895 5750 12193 37690
-groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot 1.1.2 groot 1.1.2 Up-to-date Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+graphlan graphlan, graphlan_annotate GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan graphlan GraPhlAn 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. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1285 1350 9816 10927 368 368 1273 1273 242 242 1104 1104 1895 5750 12193 37690
+groot groot GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot 1.1.2 groot 1.1.2 Up-to-date Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gtdb_to_taxdump gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/nick-youngblut/gtdb_to_taxdump https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-gtdbtk gtdbtk_classify_wf 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. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.4.0 gtdbtk 2.4.0 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk GTDB-Tk GTDB-Tk 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). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87 87 476 476 0 0 0 0 74 74 588 588 161 483 1064 3192
-gtftobed12 gtftobed12 Convert GTF files to BED12 format 2018-05-17 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README 357 ucsc-gtftogenepred 469 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3336 3828 8329 9363 3130 3130 8009 8009 344 344 1577 1577 6810 20922 17915 54779
-gubbins gubbins Gubbins - bacterial recombination detection 2017-06-22 3.2.1 gubbins 3.4 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 326 336 3690 3811 235 235 3323 3323 234 258 1895 2429 795 2419 8908 27379
+gtdbtk gtdbtk_classify_wf 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. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.4.0 gtdbtk 2.4.0 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk GTDB-Tk GTDB-Tk 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). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87 87 476 476 0 0 0 0 74 74 588 588 161 483 1064 3192
+gtftobed12 gtftobed12 Convert GTF files to BED12 format 2018-05-17 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README 357 ucsc-gtftogenepred 469 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3336 3828 8329 9363 3130 3130 8009 8009 344 344 1577 1577 6810 20922 17915 54779
+gubbins gubbins Gubbins - bacterial recombination detection 2017-06-22 3.2.1 gubbins 3.4 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 326 336 3690 3811 235 235 3323 3323 234 258 1895 2429 795 2419 8908 27379
halfdeep halfdeep HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. 2024-11-27 https://github.com/makovalab-psu/HalfDeep 0.1.0 halfdeep 0.1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.1.4 Up-to-date Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 222 222 7303 7303 2 2 20 20 0 0 0 0 224 672 7323 21969
+hamronization hamronize_summarize, hamronize_tool Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.1.4 Up-to-date Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 222 222 7303 7303 2 2 20 20 0 0 0 0 224 672 7323 21969
hapcut2 hapcut2 Robust and accurate haplotype assembly for diverse sequencing technologies 2022-10-19 https://github.com/vibansal/HapCUT2 1.3.4 hapcut2 1.3.4 Up-to-date Assembly Haplotype mapping, Variant classification Haplotype mapping, Variant classification galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 103 103 4 12 103 309
-hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes 2022-09-16 https://github.com/institut-de-genomique/HAPO-G 1.3.8 hapog 1.3.8 Up-to-date Assembly Genome assembly, Optimisation and refinement Genome assembly, Optimisation and refinement Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 66 66 502 502 0 0 0 0 0 0 0 0 66 198 502 1506
+hapog hapog Hapo-G - Haplotype-Aware Polishing of Genomes 2022-09-16 https://github.com/institut-de-genomique/HAPO-G 1.3.8 hapog 1.3.8 Up-to-date Assembly Genome assembly, Optimisation and refinement Genome assembly, Optimisation and refinement Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 66 66 502 502 0 0 0 0 0 0 0 0 66 198 502 1506
happy som.py A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. 2022-01-25 https://github.com/Illumina/hap.py 0.3.14 hap.py 0.3.15 To update Variant Analysis Variant calling, Sequence analysis, Genotyping Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism Genomics, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
heinz heinz_bum, heinz, heinz_scoring, heinz_visualization An algorithm for identification of the optimal scoring subnetwork. 2018-06-11 https://github.com/ls-cwi/heinz 1.0 bioconductor-bionet 1.62.0 To update Transcriptomics, Visualization, Statistics, Single Cell Pathway or network analysis Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks Genetics, Gene expression, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz heinz Heinz Tool for single-species active module discovery. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 367 442 1281 1434 636 636 1559 1559 52 52 678 678 1055 3240 3518 10707
hgvsparser hgvsparser Parsing and building variant descriptor strings compliant with the HGVS standard 2024-06-07 https://github.com/VariantEffect/hgvsParseR/tree/master 0.1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 6346 6346 0 0 0 0 0 0 0 0 2 6 6346 19038
-hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 2017-08-24 https://github.com/deeptools/HiCExplorer 3.7.6 hicexplorer 3.7.6 Up-to-date Sequence Analysis, Visualization bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 38 38 38 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 3236 4177 44449 68602 21 21 46 46 67 67 1328 1328 3324 10913 45823 161622
-hifiasm hifiasm A fast haplotype-resolved de novo assembler 2024-07-11 https://github.com/chhylp123/hifiasm 0.20.0 hifiasm 0.23.0 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 539 539 1819 1819 389 389 1334 1334 137 137 2472 2472 1065 3195 5625 16875
+hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 2017-08-24 https://github.com/deeptools/HiCExplorer 3.7.6 hicexplorer 3.7.6 Up-to-date Sequence Analysis, Visualization bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer 38 38 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 33 36 33 0 3236 4177 44449 68602 21 21 46 46 67 67 1328 1328 3324 10913 45823 161622
+hifiasm hifiasm A fast haplotype-resolved de novo assembler 2024-07-11 https://github.com/chhylp123/hifiasm 0.20.0 hifiasm 0.23.0 To update Assembly bgruening https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 539 539 1819 1819 389 389 1334 1334 137 137 2472 2472 1065 3195 5625 16875
hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 156 156 0 0 0 0 11 11 220 220 31 93 376 1128
-hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. 2015-09-29 http://ccb.jhu.edu/software/hisat2/ 2.2.1 hisat2 2.2.1 Up-to-date Assembly Sequence alignment Sequence alignment RNA-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10046 10719 337151 353499 26656 34018 699868 896164 5302 5695 87016 94859 42004 134440 1124035 3592592
+hisat2 hisat2 HISAT2 is a fast and sensitive spliced alignment program. 2015-09-29 http://ccb.jhu.edu/software/hisat2/ 2.2.1 hisat2 2.2.1 Up-to-date Assembly Sequence alignment Sequence alignment RNA-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 10046 10719 337151 353499 26656 34018 699868 896164 5302 5695 87016 94859 42004 134440 1124035 3592592
hivclustering hivclustering Infers transmission networks from pairwise distances inferred by tn93 2018-06-06 https://pypi.org/project/hivclustering/ 1.3.1 python-hivclustering 1.8.0 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) 2016-09-15 https://readthedocs.org/projects/htseq/ 2.0.5 htseq 2.0.5 Up-to-date Genomic Interval Operations, SAM, Sequence Analysis, RNA Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3703 4366 144907 168824 10798 16485 213407 346792 2613 2854 27209 33124 17114 57933 385523 1319786
-humann 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 HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann humann humann 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 “What are the microbes in my community-of-interest doing (or are capable of doing)?” 6 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 2067 2067 26659 26659 174 174 865 865 351 351 3238 3238 2592 7776 30762 92286
+htseq_count htseq_count Count aligned reads (SAM/BAM) that overlap genomic features (GFF) 2016-09-15 https://readthedocs.org/projects/htseq/ 2.0.5 htseq 2.0.5 Up-to-date Genomic Interval Operations, SAM, Sequence Analysis, RNA Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis lparsons https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3703 4366 144907 168824 10798 16485 213407 346792 2613 2854 27209 33124 17114 57933 385523 1319786
+humann 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 HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann humann humann 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 “What are the microbes in my community-of-interest doing (or are capable of doing)?” 6 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 2067 2067 26659 26659 174 174 865 865 351 351 3238 3238 2592 7776 30762 92286
hybpiper hybpiper Analyse targeted sequence capture data 2023-08-30 https://github.com/mossmatters/HybPiper 2.1.6 hybpiper 2.3.1 To update Sequence Analysis, Phylogenetics Sequence trimming, Sequence assembly, Read mapping Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 1571 1571 0 0 0 0 4 4 144 144 7 21 1715 5145
hypo hypo Super Fast & Accurate Polisher for Long Read Genome Assemblies 2021-11-15 https://github.com/kensung-lab/hypo 1.0.3 hypo 1.0.3 Up-to-date Assembly Optimisation and refinement, Genome assembly Optimisation and refinement, Genome assembly Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo HyPo HyPo 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 93 93 473 473 0 0 0 0 0 0 0 0 93 279 473 1419
-icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. 2022-01-04 https://icescreen.migale.inrae.fr/ 1.3.1 icescreen 1.3.2 To update Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-idba idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba IDBA 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. 3 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 187 195 1200 1220 267 267 1588 1588 0 0 0 0 454 1370 2788 8384
+icescreen icescreen ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes. 2022-01-04 https://icescreen.migale.inrae.fr/ 1.3.1 icescreen 1.3.2 To update Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://forgemia.inra.fr/ices_imes_analysis/icescreen https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+idba idba_hybrid, idba_tran, idba_ud Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud idba IDBA 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. 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 187 195 1200 1220 267 267 1588 1588 0 0 0 0 454 1370 2788 8384
idr idr Galaxy wrappers for the IDR package from Nathan Boleu 2017-08-21 https://github.com/nboley/idr 2.0.3 idr 2.0.4.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 109 114 2953 3027 199 199 1710 1710 0 0 0 0 308 929 4663 14063
-idr_download_by_ids idr_download_by_ids Image Data Resource downloading tool 2020-02-04 https://idr.openmicroscopy.org 0.45 omero-py 5.11.1 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 37 404 404 0 0 0 0 1 1 24 24 38 114 428 1284
+idr_download_by_ids idr_download_by_ids Image Data Resource downloading tool 2020-02-04 https://idr.openmicroscopy.org 0.45 omero-py 5.11.1 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 37 404 404 0 0 0 0 1 1 24 24 38 114 428 1284
iedb_api iedb_api Get epitope binding predictions from IEDB-API 2020-02-26 http://tools.immuneepitope.org/main/tools-api/ 2.15.2 python To update Data Source, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 35 1539 1539 0 0 0 0 0 0 0 0 35 105 1539 4617
infercnv infercnv Infer Copy Number Variation from Single-Cell RNA-Seq Data 2024-07-23 https://github.com/broadinstitute/infercnv 1.20.0 bioconductor-infercnv 1.20.0 Up-to-date Transcriptomics, Variant Analysis, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 10 10 0 0 0 0 0 0 0 0 2 6 10 30
instrain instrain_compare, instrain_profile InStrain is a tool for analysis of co-occurring genome populations from metagenomes 2021-08-11 https://instrain.readthedocs.io/en/latest/# 1.5.3 instrain 1.9.0 To update Metagenomics SNP detection, Genome comparison SNP detection, Genome comparison Mapping, Metagenomics Mapping, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain instrain InStrain 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 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 16 16 102 102 0 0 0 0 0 0 0 0 16 48 102 306
-integronfinder integron_finder """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""" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.5 Up-to-date Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 161 161 55149 55149 0 0 0 0 73 73 6085 6085 234 702 61234 183702
+integronfinder integron_finder """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""" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.5 Up-to-date Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 161 161 55149 55149 0 0 0 0 73 73 6085 6085 234 702 61234 183702
intermine_galaxy_exchange galaxy_intermine_exchange InterMine Exporter 2018-07-01 https://github.com/intermine 0.0.1 coreutils 8.25 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 6 12 37 46 13 15 72 87 1 1 108 108 20 68 217 675
-interproscan interproscan Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1634 1713 34689 55189 15 15 65 65 607 607 10897 10897 2256 6847 45651 157453
-interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals 2020-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.13.0 To update Genomic Interval Operations Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. 1 1 1 1 0 1 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 0 7 10 32 107 87 1246 758 19538 2 2 16 24 96 1450 806 21281
+interproscan interproscan Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1634 1713 34689 55189 15 15 65 65 607 607 10897 10897 2256 6847 45651 157453
+interval2maf Interval2Maf1 Extract MAF blocks given a set of intervals 2020-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1+galaxy1 bx-python 0.13.0 To update Genomic Interval Operations Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 7 10 32 107 87 1246 758 19538 2 2 16 24 96 1450 806 21281
intervene intervene_pairwise, intervene_upset Create pairwise and upset plots 2018-09-11 https://intervene.readthedocs.io 0.6.5 intervene 0.6.5 Up-to-date Statistics Sequence comparison, Sequence visualisation Sequence comparison, Sequence visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 278 292 1557 1607 458 458 4458 4458 0 0 0 0 736 2222 6015 18095
-iqtree iqtree Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.3.6 iqtree 2.3.6 Up-to-date Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree iqtree iqtree 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 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1623 1646 28279 28481 2093 2093 24662 24662 979 992 9780 10086 4695 14121 62721 188671
+iqtree iqtree Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.3.6 iqtree 2.3.6 Up-to-date Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree iqtree iqtree 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 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1623 1646 28279 28481 2093 2093 24662 24662 979 992 9780 10086 4695 14121 62721 188671
irissv irissv Refine insertion sequences 2021-01-17 https://github.com/mkirsche/Iris 1.0.5 samtools 1.21 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tools/irissv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 8 29 29 0 0 0 0 0 0 0 0 8 24 29 87
irma irma Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. 2024-11-09 https://wonder.cdc.gov/amd/flu/irma/irma.html 1.2.0 irma 1.2.0 Up-to-date Sequence Analysis Mapping assembly Mapping assembly iuc https://github.com/aaronKol/tools-iuc/tree/main/tools/irma https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma irma-virus IRMA Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. 2022-12-17 https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 To update Transcriptomics, RNA, Statistics Sequence comparison, Sequence analysis Sequence comparison, Sequence analysis Computational biology, Gene transcripts Computational biology, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 1301 1301 60 60 1331 1331 9 9 507 507 128 384 3139 9417
-ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing 2020-03-21 https://github.com/andersen-lab/ivar 1.4.3 ivar 1.4.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 4 0 0 0 0 0 0 5 5 5 0 2366 2366 1252220 1252220 2496 2496 126027 126027 993 993 41901 41901 5855 17565 1420148 4260444
+isoformswitchanalyzer isoformswitchanalyzer Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. 2022-12-17 https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html 1.20.0 bioconductor-isoformswitchanalyzer 2.2.0 To update Transcriptomics, RNA, Statistics Sequence comparison, Sequence analysis Sequence comparison, Sequence analysis Computational biology, Gene transcripts Computational biology, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 1301 1301 60 60 1331 1331 9 9 507 507 128 384 3139 9417
+ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing 2020-03-21 https://github.com/andersen-lab/ivar 1.4.3 ivar 1.4.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 4 0 0 0 0 0 0 5 5 5 0 2366 2366 1252220 1252220 2496 2496 126027 126027 993 993 41901 41901 5855 17565 1420148 4260444
iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot Interval-Wise Testing for Omics Data 2017-06-08 https://bioconductor.org/packages/release/bioc/html/IWTomics.html 1.0.0 bioconductor-iwtomics 1.26.0 To update Statistics Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 27 28 675 690 29 49 159 251 12 12 383 383 68 225 1217 3758
jasminesv jasminesv Merge structural variants across samples 2021-01-17 https://github.com/mkirsche/Jasmine/ 1.0.11 jasminesv 1.1.5 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/jasminesv/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 9 32 32 19 19 53 53 0 0 0 0 28 84 85 255
-jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool 2015-05-01 https://jbrowse.org 1.16.11 jbrowse 1.16.11 Up-to-date Sequence Analysis Genome visualisation Genome visualisation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse jbrowse JBrowse 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. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 5514 5779 21153 22174 6458 6458 17428 17428 3248 3786 15673 17267 15220 46463 54254 165377
-jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 2018-07-31 https://github.com/tanghaibao/jcvi 0.8.4 jcvi 1.4.16 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 596 637 2747 2926 741 741 2311 2311 469 469 1145 1145 1806 5459 6203 18788
-jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 237 237 1825 1825 0 0 0 0 56 56 971 971 293 879 2796 8388
-join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier 2017-05-31 https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-jq jq JQ is a lightweight and flexible command-line JSON processor 2017-06-22 https://stedolan.github.io/jq/ 1.0 jq 1.5 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61 63 660 2374 82 82 336 336 11 11 281 281 154 464 1277 5545
-jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics 2021-02-11 https://lindenb.github.io/jvarkit/ 20201223 jvarkit-wgscoverageplotter 20201223 Up-to-date SAM iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 509 509 7179 7179 1145 1145 11138 11138 0 0 0 0 1654 4962 18317 54951
+jbrowse jbrowse_to_standalone, jbrowse JBrowse Genome Browser integrated as a Galaxy Tool 2015-05-01 https://jbrowse.org 1.16.11 jbrowse 1.16.11 Up-to-date Sequence Analysis Genome visualisation Genome visualisation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse jbrowse JBrowse 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. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 5514 5779 21153 22174 6458 6458 17428 17428 3248 3786 15673 17267 15220 46463 54254 165377
+jcvi_gff_stats jcvi_gff_stats Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 2018-07-31 https://github.com/tanghaibao/jcvi 0.8.4 jcvi 1.4.16 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 596 637 2747 2926 741 741 2311 2311 469 469 1145 1145 1806 5459 6203 18788
+jellyfish jellyfish Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 237 237 1825 1825 0 0 0 0 56 56 971 971 293 879 2796 8388
+join_files_by_id join_files_by_id This tool will join datasets according to a column with identifier 2017-05-31 https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+jq jq JQ is a lightweight and flexible command-line JSON processor 2017-06-22 https://stedolan.github.io/jq/ 1.0 jq 1.5 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 61 63 660 2374 82 82 336 336 11 11 281 281 154 464 1277 5545
+jvarkit jvarkit_wgscoverageplotter Jvarkit : Java utilities for Bioinformatics 2021-02-11 https://lindenb.github.io/jvarkit/ 20201223 jvarkit-wgscoverageplotter 20201223 Up-to-date SAM iuc https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 509 509 7179 7179 1145 1145 11138 11138 0 0 0 0 1654 4962 18317 54951
kc_align kc-align Kc-Align custom tool 2020-02-20 https://github.com/davebx/kc-align 1.0.2 kcalign 1.0.2 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 53 53 379 379 271 271 8259 8259 0 0 0 0 324 972 8638 25914
-khmer 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 In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer khmer khmer 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. 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 174 193 1995 2091 389 389 1430 1430 56 56 1580 1580 619 1876 5005 15111
+khmer 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 In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer khmer khmer 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. 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 8 8 8 0 174 193 1995 2091 389 389 1430 1430 56 56 1580 1580 619 1876 5005 15111
king king Kinship-based INference for Gwas 2021-11-16 http://people.virginia.edu/~wc9c/KING/ 2.2.7 king 2.2.7 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/king 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 8 8 0 0 0 0 0 0 0 0 4 12 8 24
-kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate/wiki 2.3.2 kleborate 3.1.2 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate kleborate Kleborate 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). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 58 58 503 503 0 0 0 0 0 0 0 0 58 174 503 1509
+kleborate kleborate Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate/wiki 2.3.2 kleborate 3.1.2 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/katholt/Kleborate https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate kleborate Kleborate 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). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 58 58 503 503 0 0 0 0 0 0 0 0 58 174 503 1509
kma kma_map Map with KMA 2019-10-30 https://bitbucket.org/genomicepidemiology/kma 1.4.14 kma 1.4.15 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
-kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan 1.3.0 kofamscan 1.3.0 Up-to-date Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 63 63 1342 1342 0 0 0 0 0 0 0 0 63 189 1342 4026
-kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken 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. 2017-01-24 http://ccb.jhu.edu/software/kraken/ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken Kraken 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. 5 5 5 5 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 2754 2760 48136 48164 5869 8654 59952 130398 1936 2200 29008 31148 10559 34732 137096 483902
-kraken2 kraken2 Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.1.3 kraken2 2.1.3 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 kraken2 kraken2 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 6384 6409 271367 271786 4662 4662 101752 101752 1663 1663 53562 53562 12709 38152 426681 1280462
-kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) 2022-09-03 https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 Up-to-date Metagenomics iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 495 495 3185 3185 0 0 0 0 48 48 385 385 543 1629 3570 10710
+kofamscan kofamscan Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan 1.3.0 kofamscan 1.3.0 Up-to-date Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 63 63 1342 1342 0 0 0 0 0 0 0 0 63 189 1342 4026
+kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken 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. 2017-01-24 http://ccb.jhu.edu/software/kraken/ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken Kraken 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. 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 0 5 5 5 0 2754 2760 48136 48164 5869 8654 59952 130398 1936 2200 29008 31148 10559 34732 137096 483902
+kraken2 kraken2 Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.1.3 kraken2 2.1.3 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 kraken2 kraken2 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 6384 6409 271367 271786 4662 4662 101752 101752 1663 1663 53562 53562 12709 38152 426681 1280462
+kraken_biom kraken_biom Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) 2022-09-03 https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 Up-to-date Metagenomics iuc https://github.com/smdabdoub/kraken-biom https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 495 495 3185 3185 0 0 0 0 48 48 385 385 543 1629 3570 10710
kraken_taxonomy_report kraken_taxonomy_report Kraken taxonomy report 2016-06-01 https://github.com/blankenberg/Kraken-Taxonomy-Report 0.0.3 biopython 1.70 To update Metagenomics Visualisation, Classification Visualisation, Classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 769 771 3981 3986 991 1284 4087 5610 41 41 88 88 1801 5698 8156 25996
-krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken 2023-01-13 https://github.com/jenniferlu717/KrakenTools 1.2 krakentools 1.2 Up-to-date Metagenomics Visualisation, Aggregation Visualisation, Aggregation Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files 6 6 6 6 0 0 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 2373 2373 48516 48516 943 943 8787 8787 393 393 4369 4369 3709 11127 61672 185016
-krocus krocus Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. 2020-06-17 http://last.cbrc.jp/ 1205 last 1595 To update Sequence Analysis Sequence alignment Sequence alignment Genomics, Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last last LAST Short read alignment program incorporating quality scores 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 94 94 329 329 0 0 0 0 0 0 0 0 94 282 329 987
-lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d 2018-02-12 https://github.com/lastz/lastz 1.04.22 lastz 1.04.22 Up-to-date Next Gen Mappers Sequence alignment, Read mapping Sequence alignment, Read mapping Genomics Genomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 447 475 77409 84356 870 3511 156658 193590 173 203 38579 38780 1490 7169 272646 862018
+krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa KrakenTools is a suite of scripts to be used alongside the Kraken 2023-01-13 https://github.com/jenniferlu717/KrakenTools 1.2 krakentools 1.2 Up-to-date Metagenomics Visualisation, Aggregation Visualisation, Aggregation Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 1 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 2373 2373 48516 48516 943 943 8787 8787 393 393 4369 4369 3709 11127 61672 185016
+krocus krocus Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+last last_al, last_db, last_split, last_train, last_maf_convert LAST finds similar regions between sequences. 2020-06-17 http://last.cbrc.jp/ 1205 last 1595 To update Sequence Analysis Sequence alignment Sequence alignment Genomics, Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/last https://github.com/galaxyproject/tools-iuc/tree/main/tools/last last LAST Short read alignment program incorporating quality scores 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 94 94 329 329 0 0 0 0 0 0 0 0 94 282 329 987
+lastz lastz_wrapper_2, lastz_d_wrapper Galaxy wrappers for the Lastz and Lastz_d 2018-02-12 https://github.com/lastz/lastz 1.04.22 lastz 1.04.22 Up-to-date Next Gen Mappers Sequence alignment, Read mapping Sequence alignment, Read mapping Genomics Genomics devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 447 475 77409 84356 870 3511 156658 193590 173 203 38579 38780 1490 7169 272646 862018
lcrgenie lcrgenie Ligase Chain Reaction Genie 2022-12-02 https://github.com/neilswainston/LCRGenie 1.0.2 lcr_genie To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
legsta legsta Performs in silico Legionella pneumophila sequence based typing. 2022-02-21 https://github.com/tseemann/legsta 0.5.1 legsta 0.5.1 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Public health and epidemiology Public health and epidemiology iuc https://github.com/tseemann/legsta https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 92 92 0 0 0 0 0 0 0 0 8 24 92 276
-length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file 2016-11-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 To update Fasta Manipulation, Statistics, RNA, Micro-array Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 666 698 4349 4466 928 998 2093 2286 77 77 201 201 1671 5115 6643 20239
-limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline 2017-05-24 http://bioconductor.org/packages/release/bioc/html/limma.html 3.58.1 bioconductor-limma 3.58.1 Up-to-date Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Molecular biology, Genetics Molecular biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom limma limma Data analysis, linear models and differential expression for microarray data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2379 2475 23442 24466 4565 5032 45734 49342 835 842 9327 9517 7779 23907 78503 240331
+length_and_gc_content length_and_gc_content Gets gene length and gc content from a fasta and a GTF file 2016-11-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 To update Fasta Manipulation, Statistics, RNA, Micro-array Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 666 698 4349 4466 928 998 2093 2286 77 77 201 201 1671 5115 6643 20239
+limma_voom limma_voom Perform RNA-Seq differential expression analysis using limma voom pipeline 2017-05-24 http://bioconductor.org/packages/release/bioc/html/limma.html 3.58.1 bioconductor-limma 3.62.0 To update Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Molecular biology, Genetics Molecular biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom limma limma Data analysis, linear models and differential expression for microarray data. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2379 2475 23442 24466 4565 5032 45734 49342 835 842 9327 9517 7779 23907 78503 240331
lineagespot lineagespot Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) 2023-07-04 https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html 1.6.0 r-base To update Metagenomics, Sequence Analysis Variant calling Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot lineagespot lineagespot 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). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 39 39 0 0 0 0 0 0 0 0 4 12 39 117
-links links Scaffold genome assemblies with long reads. 2022-02-23 https://github.com/bcgsc/LINKS 2.0.1 links 2.0.1 Up-to-date Assembly Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 512 512 0 0 0 0 65 65 480 480 191 573 992 2976
+links links Scaffold genome assemblies with long reads. 2022-02-23 https://github.com/bcgsc/LINKS 2.0.1 links 2.0.1 Up-to-date Assembly Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/links https://github.com/galaxyproject/tools-iuc/tree/main/tools/links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 126 126 512 512 0 0 0 0 65 65 480 480 191 573 992 2976
lorikeet_spoligotype lorikeet_spoligotype Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 2018-05-07 https://github.com/AbeelLab/lorikeet 20 lorikeet 20 Up-to-date Sequence Analysis Sequence analysis, Genotyping Sequence analysis, Genotyping Genotype and phenotype Genotype and phenotype iuc https://github.com/AbeelLab/lorikeet https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 14 822 822 0 0 0 0 0 0 0 0 14 42 822 2466
lumpy_sv lumpy_prep, lumpy_sv LUMPY - a general probabilistic framework for structural variant discovery 2020-11-12 http://layerlab.org/software/ 0.3.1 lumpy-sv 0.3.1 Up-to-date Variant Analysis iuc https://github.com/arq5x/lumpy-sv https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 199 199 1534 1534 0 0 0 0 0 0 0 0 199 597 1534 4602
m6anet m6anet m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest 2.1.0 m6anet 2.1.0 Up-to-date Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 11 44 44 0 0 0 0 0 0 0 0 11 33 44 132
maaslin2 maaslin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. 2021-11-05 http://huttenhower.sph.harvard.edu/maaslin 1.18.0 bioconductor-maaslin2 1.18.0 Up-to-date Metagenomics Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Metagenomics, Statistics and probability iuc https://github.com/biobakery/Maaslin2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 59 59 2835 2835 0 0 0 0 0 0 0 0 59 177 2835 8505
-macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq 2014-11-12 https://github.com/taoliu/MACS 2.2.9.1 macs2 2.2.9.1 Up-to-date Sequence Analysis, Statistics Peak calling, Enrichment analysis, Gene regulatory network analysis Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 macs MACS Model-based Analysis of ChIP-seq data. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 4980 5629 87810 96069 12946 18825 153500 227569 692 807 10988 12301 18618 62497 252298 840535
-maf_stats maf_stats1 MAF Coverage statistics 2020-08-12 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1 1 1 1 0 1 0 0 0 1 0 0 0 1 1 1 0 1 0 0 0 0 1 1 0 0 0 0 1 1 1 1 1 0 7 9 15 21 52 464 227 2470 1 1 1 1 60 594 243 2978
+macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak MACS - Model-based Analysis of ChIP-Seq 2014-11-12 https://github.com/taoliu/MACS 2.2.9.1 macs2 2.2.9.1 Up-to-date Sequence Analysis, Statistics Peak calling, Enrichment analysis, Gene regulatory network analysis Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 macs MACS Model-based Analysis of ChIP-seq data. 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 9 9 0 0 0 0 0 0 9 0 0 0 0 0 0 9 9 9 0 4980 5629 87810 96069 12946 18825 153500 227569 692 807 10988 12301 18618 62497 252298 840535
+maf_stats maf_stats1 MAF Coverage statistics 2020-08-12 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2+galaxy0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats 1 1 1 0 0 1 0 0 0 1 1 0 0 0 1 1 1 0 1 0 0 0 0 1 0 0 0 0 1 1 1 1 1 0 7 9 15 21 52 464 227 2470 1 1 1 1 60 594 243 2978
magicblast magicblast Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome 2022-04-05 https://ncbi.github.io/magicblast/ 1.7.0 magicblast 1.7.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 151 151 738 738 0 0 0 0 1 1 2 2 152 456 740 2220
malt_run malt_run Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. 2021-11-12 https://github.com/husonlab/malt 0.5.3 malt 0.62 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 24 24 0 0 0 0 0 0 0 0 9 27 24 72
map_param_value map_param_value Map a parameter value to another value 2022-10-13 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 67 3780 3780 57 57 1012 1012 3 3 105 105 127 381 4897 14691
-mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq 2.1.1b perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 7871 7871 0 0 0 0 0 0 0 0 32 96 7871 23613
+mapseq mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq 2.1.1b perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 32 32 7871 7871 0 0 0 0 0 0 0 0 32 96 7871 23613
mashmap mashmap Fast local alignment boundaries 2024-02-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap 3.1.3 mashmap 3.1.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 894 894 5 5 81 81 0 0 0 0 17 51 975 2925
masigpro masigpro Identify significantly differential expression profiles in time-course microarray experiments 2017-05-09 https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html 1.49.3 coreutils 8.25 To update Transcriptomics, RNA, Statistics Regression analysis Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Gene expression, Microarray experiment, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 40 471 582 80 80 589 589 0 0 0 0 115 350 1060 3291
-maxbin2 maxbin2 clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 314 314 2798 2798 508 508 2452 2452 89 89 914 914 911 2733 6164 18492
+maxbin2 maxbin2 clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 314 314 2798 2798 508 508 2452 2452 89 89 914 914 911 2733 6164 18492
mcl mcl The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html 22.282 mcl 22.282 Up-to-date Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 13 13 35 35 0 0 0 0 0 0 0 0 13 39 35 105
-megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2017-09-22 https://github.com/voutcn/megahit 1.2.9 megahit 1.2.9 Up-to-date Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit megahit MEGAHIT 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 1349 1400 12692 13292 2140 2140 16645 16645 431 431 6214 6214 3920 11811 35551 107253
-megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-09 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp 1.1.3 megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg megahit MEGAHIT 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 152 155 513 557 35 35 74 74 4 4 10 10 191 576 597 1835
+megahit megahit An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2017-09-22 https://github.com/voutcn/megahit 1.2.9 megahit 1.2.9 Up-to-date Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit megahit MEGAHIT 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 1349 1400 12692 13292 2140 2140 16645 16645 431 431 6214 6214 3920 11811 35551 107253
+megahit_contig2fastg megahit_contig2fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-09 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp 1.1.3 megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg megahit MEGAHIT 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 152 155 513 557 35 35 74 74 4 4 10 10 191 576 597 1835
megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma 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). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.9 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 447 447 4130 4130 0 0 0 0 0 0 0 0 447 1341 4130 12390
-meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. 2015-12-13 http://meme-suite.org/ 5.5.6 meme 5.5.7 To update ChIP-seq Nucleic acid feature detection, Protein feature detection, Statistical calculation Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability Data mining, Sequence analysis, Genetic variation, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. 3 0 4 0 0 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 762 892 20990 22979 1551 3249 10975 25929 0 0 0 0 2313 8767 31965 112838
-meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 2018-03-15 http://meme-suite.org/ 4.11.2 graphicsmagick 1.3.26 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 705 743 6413 7000 1171 1171 7260 7260 0 0 0 0 1876 5666 13673 41606
+meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. 2015-12-13 http://meme-suite.org/ 5.5.6 meme 5.5.7 To update ChIP-seq Nucleic acid feature detection, Protein feature detection, Statistical calculation Nucleic acid feature detection, Protein feature detection, Statistical calculation Data mining, Sequence analysis, Genetic variation, Statistics and probability Data mining, Sequence analysis, Genetic variation, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme meme_meme meme_meme An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. 3 0 4 0 0 0 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 4 0 762 892 20990 22979 1551 3249 10975 25929 0 0 0 0 2313 8767 31965 112838
+meme_chip meme_chip Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 2018-03-15 http://meme-suite.org/ 4.11.2 graphicsmagick 1.3.26 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 705 743 6413 7000 1171 1171 7260 7260 0 0 0 0 1876 5666 13673 41606
meningotype meningotype Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype 0.8.5 meningotype 0.8.5 Up-to-date Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
merlin merlin Pedigree Analysis package 2020-04-15 http://csg.sph.umich.edu/abecasis/Merlin/ 1.1.2 merlin 1.1.2 Up-to-date Variant Analysis Haplotype mapping, Genetic mapping Haplotype mapping GWAS study, Mapping GWAS study, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 2021-04-18 https://github.com/marbl/merqury 1.3 merqury 1.3 Up-to-date Assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Sequence assembly, Whole genome sequencing, Plant biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury merqury Merqury 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. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 477 477 3150 3150 196 196 730 730 151 151 1183 1183 824 2472 5063 15189
+merqury merqury, merquryplot Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 2021-04-18 https://github.com/marbl/merqury 1.3 merqury 1.3 Up-to-date Assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Sequence assembly, Whole genome sequencing, Plant biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury merqury Merqury 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. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 477 477 3150 3150 196 196 730 730 151 151 1183 1183 824 2472 5063 15189
meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode Meryl a k-mer counter. 2021-04-05 https://github.com/marbl/meryl 1.3 merqury 1.3 Up-to-date Assembly k-mer counting k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Whole genome sequencing, Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl meryl Meryl 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. 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 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. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.15 metabat2 2.17 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 MetaBAT_2 MetaBAT 2 "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" 2 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 382 382 6135 6135 151 151 881 881 104 104 1094 1094 637 1911 8110 24330
+metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 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. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.15 metabat2 2.17 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 MetaBAT_2 MetaBAT 2 "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" 2 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 382 382 6135 6135 151 151 881 881 104 104 1094 1094 637 1911 8110 24330
metabuli metabuli_classify Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences 2024-06-04 https://github.com/steineggerlab/Metabuli 1.0.5 metabuli 1.0.8 To update Sequence Analysis, Metagenomics Taxonomic classification Taxonomic classification Taxonomy Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-metagenomeseq_normalization metagenomeseq_normalizaton metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq metagenomeseq metagenomeSeq 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. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 17 21 556 756 35 55 310 514 0 0 0 0 52 180 866 3002
-metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.1.1 metaphlan 4.1.1 Up-to-date Metagenomics Nucleic acid sequence analysis, Phylogenetic tree analysis Nucleic acid sequence analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. 1 2 4 4 0 0 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1183 1187 16629 16648 572 572 3983 3983 278 278 4747 4747 2033 6103 25359 76096
+metagenomeseq_normalization metagenomeseq_normalizaton metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq metagenomeseq metagenomeSeq 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 17 21 556 756 35 55 310 514 0 0 0 0 52 180 866 3002
+metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.1.1 metaphlan 4.1.1 Up-to-date Metagenomics Nucleic acid sequence analysis, Phylogenetic tree analysis Nucleic acid sequence analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. 1 2 4 0 0 0 0 0 0 0 0 0 0 0 0 2 0 4 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 0 1183 1187 16629 16648 572 572 3983 3983 278 278 4747 4747 2033 6103 25359 76096
metawrapmg_binning metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis 2024-04-11 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg 1.3.0 Up-to-date Metagenomics Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg metawrap MetaWRAP 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. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 32 142 142 0 0 0 0 47 47 379 379 79 237 521 1563
mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
microsatbed microsatbed Select microsatellites for a bed file 2024-07-21 https://github.com/lmdu/pytrf 1.3.3 python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 228 228 1 1 18 18 0 0 0 0 5 15 246 738
-migmap migmap mapper for full-length T- and B-cell repertoire sequencing 2017-09-29 https://github.com/mikessh/migmap 1.0.3 migmap 1.0.3 Up-to-date RNA, Sequence Analysis Sequence analysis, Read mapping Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 33 1082 1229 70 89 1153 1376 0 0 0 0 95 312 2235 7075
-minia minia Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ 3.2.6 minia 3.2.6 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 256 256 7116 7116 0 0 0 0 60 60 278 278 316 948 7394 22182
-miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm 0.3_r179 miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm miniasm miniasm 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 562 13357 13479 448 448 8416 8416 85 85 898 898 1087 3269 22671 68135
-minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 2017-11-03 https://github.com/lh3/minimap2 2.28 minimap2 2.28 Up-to-date Next Gen Mappers Pairwise sequence alignment Pairwise sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4323 4419 346530 349075 4075 4075 108535 108535 1166 1166 22331 22331 9564 28788 477396 1434733
+migmap migmap mapper for full-length T- and B-cell repertoire sequencing 2017-09-29 https://github.com/mikessh/migmap 1.0.3 migmap 1.0.3 Up-to-date RNA, Sequence Analysis Sequence analysis, Read mapping Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 25 33 1082 1229 70 89 1153 1376 0 0 0 0 95 312 2235 7075
+minia minia Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ 3.2.6 minia 3.2.6 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 256 256 7116 7116 0 0 0 0 60 60 278 278 316 948 7394 22182
+miniasm miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm 0.3_r179 miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm miniasm miniasm 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 554 562 13357 13479 448 448 8416 8416 85 85 898 898 1087 3269 22671 68135
+minimap2 minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences 2017-11-03 https://github.com/lh3/minimap2 2.28 minimap2 2.28 Up-to-date Next Gen Mappers Pairwise sequence alignment Pairwise sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 4323 4419 346530 349075 4075 4075 108535 108535 1166 1166 22331 22331 9564 28788 477396 1434733
mirmachine mirmachine Tool to detect miRNA in genome sequences 2024-03-15 https://github.com/sinanugur/MirMachine 0.2.13 mirmachine 0.2.13 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 6 2 6
mirnature mirnature Computational detection of canonical microRNAs 2022-12-11 https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 Up-to-date RNA, Sequence Analysis iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 9 9 18 18 0 0 0 0 0 0 0 0 9 27 18 54
-mitobim mitobim assemble mitochondrial genomes 2020-12-29 https://github.com/chrishah/MITObim 1.9.1 mitobim 1.9.1 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 116 116 1117 1117 0 0 0 0 25 25 295 295 141 423 1412 4236
-mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ 1.1.7 mitos 2.1.9 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 1111 1111 191295 191295 320 320 42265 42265 83 83 10904 10904 1514 4542 244464 733392
-mlst mlst, mlst_list Scan contig files against PubMLST typing schemes 2016-12-12 https://github.com/tseemann/mlst 2.22.0 mlst 2.23.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1480 1501 13300 13471 1167 1167 6532 6532 1083 1300 10334 11841 3730 11428 30166 92176
+mitobim mitobim assemble mitochondrial genomes 2020-12-29 https://github.com/chrishah/MITObim 1.9.1 mitobim 1.9.1 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 116 116 1117 1117 0 0 0 0 25 25 295 295 141 423 1412 4236
+mitos mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ 1.1.7 mitos 2.1.9 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 1111 1111 191295 191295 320 320 42265 42265 83 83 10904 10904 1514 4542 244464 733392
+mlst mlst, mlst_list Scan contig files against PubMLST typing schemes 2016-12-12 https://github.com/tseemann/mlst 2.22.0 mlst 2.23.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1480 1501 13300 13471 1167 1167 6532 6532 1083 1300 10334 11841 3730 11428 30166 92176
moabs moabs MOABS for differential methylation analysis on Bisulfite sequencing data. 2019-07-28 https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.0 To update Epigenetics iuc https://github.com/sunnyisgalaxy/moabs https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 56 56 339 339 0 0 0 0 0 0 0 0 56 168 339 1017
-mosdepth mosdepth fast and flexible BAM/CRAM depth calculation 2022-12-04 https://github.com/brentp/mosdepth 0.3.10 mosdepth 0.3.10 Up-to-date SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 87 87 1278 1278 24 24 168 168 5 5 102 102 116 348 1548 4644
-mothur 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 Mothur wrappers 2016-06-24 https://www.mothur.org 1.0 mothur 1.48.0 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Microbial ecology, Taxonomy, Sequence analysis, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities 129 129 129 129 0 0 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 37506 41763 297546 326056 72163 89926 565218 682083 26963 28404 167400 182490 136632 433357 1030164 3250957
+mosdepth mosdepth fast and flexible BAM/CRAM depth calculation 2022-12-04 https://github.com/brentp/mosdepth 0.3.10 mosdepth 0.3.10 Up-to-date SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 87 87 1278 1278 24 24 168 168 5 5 102 102 116 348 1548 4644
+mothur 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 Mothur wrappers 2016-06-24 https://www.mothur.org 1.0 mothur 1.48.0 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Microbial ecology, Taxonomy, Sequence analysis, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities 129 129 129 0 0 0 0 0 0 0 0 0 0 0 0 128 0 3 0 0 0 0 0 0 0 0 0 0 0 0 126 129 129 0 37506 41763 297546 326056 72163 89926 565218 682083 26963 28404 167400 182490 136632 433357 1030164 3250957
msaboot msaboot A multiple sequences alignment bootstrapping tool. 2018-02-12 https://github.com/phac-nml/msaboot 0.1.2 msaboot 0.1.2 Up-to-date Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 91 101 864 929 175 175 1100 1100 0 0 0 0 266 808 1964 5957
multigps multigps Analyzes collections of multi-condition ChIP-seq data. 2017-03-06 http://mahonylab.org/software/multigps/ 0.74.0 fonts-conda-ecosystem To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 159 298 485 871 0 0 0 0 159 616 485 1841
multigsea multigsea GSEA-based pathway enrichment analysis for multi-omics data 2023-06-07 https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html 1.12.0 bioconductor-multigsea 1.12.0 Up-to-date Transcriptomics, Proteomics, Statistics, Single Cell Gene-set enrichment analysis, Aggregation, Pathway analysis Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea multiGSEA multiGSEA 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 106 106 0 0 0 0 0 0 0 0 25 75 106 318
-multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.24.1 multiqc 1.25.2 To update Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc multiqc MultiQC 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 19343 20494 182221 192389 26449 29758 163961 182413 5974 6157 40663 41855 51766 159941 386845 1190347
-mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools 2018-06-28 https://github.com/mummer4/mummer 4.0.0rc1 mummer4 4.0.0rc1 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Sequence analysis, Human genetics Sequence analysis, Human genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. 6 6 6 6 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 1940 2033 21587 22119 3626 3626 29284 29284 545 545 8194 8194 6111 18426 59065 177727
+multiqc multiqc MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.24.1 multiqc 1.25.2 To update Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc multiqc MultiQC 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 19343 20494 182221 192389 26449 29758 163961 182413 5974 6157 40663 41855 51766 159941 386845 1190347
+mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords Mummer4 Tools 2018-06-28 https://github.com/mummer4/mummer 4.0.0rc1 mummer4 4.0.0rc1 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Sequence analysis, Human genetics Sequence analysis, Human genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. 6 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 1940 2033 21587 22119 3626 3626 29284 29284 545 545 8194 8194 6111 18426 59065 177727
mykrobe mykrobe_predict Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe Mykrobe Mykrobe 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mzmine_batch mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data 2023-10-21 http://mzmine.github.io/ 3.9.0 mzmine 3.9.0 Up-to-date Metabolomics Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Proteomics, Metabolomics, Proteomics experiment, Small molecules iuc https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 9 9 0 0 0 0 0 0 0 0 5 15 9 27
-nanocompore nanocompore_db, nanocompore_sampcomp 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. 2020-04-27 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore Nanocompore Nanocompore 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 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12 12 839 839 0 0 0 0 5 5 269 269 17 51 1108 3324
-nanoplot nanoplot Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot 1.43.0 nanoplot 1.43.0 Up-to-date Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot nanoplot NanoPlot 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 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5671 5755 99052 100009 3371 3371 40386 40386 2188 2188 17919 17919 11230 33774 157357 473028
-nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate 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. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 44 44 1091 1091 0 0 0 0 0 0 0 0 44 132 1091 3273
-ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2019-11-06 https://github.com/kblin/ncbi-acc-download 0.2.8 ncbi-acc-download 0.2.8 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1664 1664 6873 6873 4513 4513 17651 17651 972 972 6228 6228 7149 21447 30752 92256
-ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. 2022-01-27 https://github.com/ncbi/datasets 16.20.0 ncbi-datasets-cli To update Data Source Data handling, Sequence database search, Data retrieval Data handling, Sequence database search, Data retrieval Biological databases Biological databases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 1024 1024 4417 4417 2275 2275 6940 6940 1 1 1 1 3300 9900 11358 34074
-ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases 2022-03-22 http://www.ncbi.nlm.nih.gov/books/NBK179288/ 22.4 entrez-direct 22.4 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 3 0 0 0 0 0 2 0 3
-ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases 2015-04-14 https://www.ncbi.nlm.nih.gov/books/NBK25501/ 1.70 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 2 0 0 0 0 0 0 0 7 7 0 533 664 2794 3191 0 0 0 0 0 0 0 0 533 1730 2794 8779
-ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). 2023-09-21 https://github.com/ncbi/fcs-gx 0.5.4 ncbi-fcs-gx 0.5.4 Up-to-date Sequence Analysis Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Sequence analysis, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx ncbi_fcs NCBI fcs 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 125 125 139 139 2489 2489 0 0 0 0 165 495 2614 7842
+nanocompore nanocompore_db, nanocompore_sampcomp 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. 2020-04-27 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore Nanocompore Nanocompore 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 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 12 12 839 839 0 0 0 0 5 5 269 269 17 51 1108 3324
+nanoplot nanoplot Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot 1.43.0 nanoplot 1.43.0 Up-to-date Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot nanoplot NanoPlot 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 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 5671 5755 99052 100009 3371 3371 40386 40386 2188 2188 17919 17919 11230 33774 157357 473028
+nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate 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. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 44 44 1091 1091 0 0 0 0 0 0 0 0 44 132 1091 3273
+ncbi_acc_download ncbi_acc_download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2019-11-06 https://github.com/kblin/ncbi-acc-download 0.2.8 ncbi-acc-download 0.2.8 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1664 1664 6873 6873 4513 4513 17651 17651 972 972 6228 6228 7149 21447 30752 92256
+ncbi_datasets datasets_download_gene, datasets_download_genome NCBI datasets downloads biological sequence data across all domains of life from NCBI. 2022-01-27 https://github.com/ncbi/datasets 16.20.0 ncbi-datasets-cli To update Data Source Data handling, Sequence database search, Data retrieval Data handling, Sequence database search, Data retrieval Biological databases Biological databases iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 1024 1024 4417 4417 2275 2275 6940 6940 1 1 1 1 3300 9900 11358 34074
+ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch NCBI Entrez Direct allow fetching data from NCBI Databases 2022-03-22 http://www.ncbi.nlm.nih.gov/books/NBK179288/ 22.4 entrez-direct 22.4 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 3 0 0 0 0 0 2 0 3
+ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary NCBI Entrez E-Utilties allow fetching data from NCBI Databases 2015-04-14 https://www.ncbi.nlm.nih.gov/books/NBK25501/ 1.70 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 2 0 0 0 0 0 0 0 7 7 0 533 664 2794 3191 0 0 0 0 0 0 0 0 533 1730 2794 8779
+ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). 2023-09-21 https://github.com/ncbi/fcs-gx 0.5.4 ncbi-fcs-gx 0.5.4 Up-to-date Sequence Analysis Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Sequence analysis, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx ncbi_fcs NCBI fcs 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 26 125 125 139 139 2489 2489 0 0 0 0 165 495 2614 7842
necat necat Error correction and de-novo assembly for ONT Nanopore reads 2021-11-29 https://github.com/xiaochuanle/NECAT 0.0.1_update20200803 necat 0.0.1_update20200803 Up-to-date Assembly De-novo assembly De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 160 160 790 790 0 0 0 0 0 0 0 0 160 480 790 2370
-newick_utils newick_display Perform operations on Newick trees 2018-10-01 http://cegg.unige.ch/newick_utils 1.6+galaxy1 newick_utils 1.6 To update Visualization, Metagenomics Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Phylogeny, Genomics, Computer science iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils newick_utilities Newick Utilities 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1113 1172 33637 34195 1816 1816 16257 16257 899 899 7582 7582 3828 11543 57476 172986
+newick_utils newick_display Perform operations on Newick trees 2018-10-01 http://cegg.unige.ch/newick_utils 1.6+galaxy1 newick_utils 1.6 To update Visualization, Metagenomics Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Phylogeny, Genomics, Computer science iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils newick_utilities Newick Utilities 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1113 1172 33637 34195 1816 1816 16257 16257 899 899 7582 7582 3828 11543 57476 172986
ngmlr ngmlr CoNvex Gap-cost alignMents for Long Reads 2020-10-27 https://github.com/philres/ngmlr 0.2.7 ngmlr 0.2.7 Up-to-date Next Gen Mappers DNA mapping, Sequence alignment, Genetic variation analysis DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 49 49 1403 1403 0 0 0 0 0 0 0 0 49 147 1403 4209
-nonpareil nonpareil Estimate average coverage in metagenomic datasets 2017-11-03 http://nonpareil.readthedocs.io 3.1.1 nonpareil 3.5.5 To update Metagenomics Operation Operation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 15 107 143 20 20 148 148 0 0 0 0 33 101 255 801
-novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 2020-05-18 https://github.com/ndierckx/NOVOPlasty 4.3.1 novoplasty 4.3.5 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 337 337 7780 7780 1 1 1 1 99 99 2323 2323 437 1311 10104 30312
+nonpareil nonpareil Estimate average coverage in metagenomic datasets 2017-11-03 http://nonpareil.readthedocs.io 3.1.1 nonpareil 3.5.5 To update Metagenomics Operation Operation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 15 107 143 20 20 148 148 0 0 0 0 33 101 255 801
+novoplasty novoplasty NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 2020-05-18 https://github.com/ndierckx/NOVOPlasty 4.3.1 novoplasty 4.3.5 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 337 337 7780 7780 1 1 1 1 99 99 2323 2323 437 1311 10104 30312
nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. 2016-11-18 https://github.com/tecangenomics/nudup 2.3.3 nudup 2.3.3 Up-to-date SAM, Metagenomics, Sequence Analysis, Transcriptomics Duplication detection, Sequence analysis Duplication detection, Sequence analysis Sequencing, Genomics Sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 http://metabarcoding.org/obitools 1.2.13 obitools 1.2.13 Up-to-date Sequence Analysis Sequence analysis, Sequence analysis Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Sequence analysis, DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools obitools OBITools 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. 0 10 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 1277 1277 37598 37598 0 0 0 0 280 280 3862 3862 1557 4671 41460 124380
-ococo ococo Variant detection of SNVs 2017-12-07 https://github.com/karel-brinda/ococo 0.1.2.6 ococo 0.1.2.7 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79 93 1850 1963 194 194 1370 1370 0 0 0 0 273 833 3220 9773
-omark omark Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.0 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 158 158 0 0 0 0 0 0 0 0 12 36 158 474
-ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 2020-06-08 https://github.com/nanoporetech/ont_fast5_api/ 3.1.3 ont-fast5-api 4.1.3 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 87 87 3051 3051 0 0 0 0 0 0 0 0 87 261 3051 9153
+obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 http://metabarcoding.org/obitools 1.2.13 obitools 1.2.13 Up-to-date Sequence Analysis Sequence analysis, Sequence analysis Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Sequence analysis, DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools obitools OBITools 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. 0 10 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 10 0 1277 1277 37598 37598 0 0 0 0 280 280 3862 3862 1557 4671 41460 124380
+ococo ococo Variant detection of SNVs 2017-12-07 https://github.com/karel-brinda/ococo 0.1.2.6 ococo 0.1.2.7 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 79 93 1850 1963 194 194 1370 1370 0 0 0 0 273 833 3220 9773
+omark omark Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.0 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 158 158 0 0 0 0 0 0 0 0 12 36 158 474
+ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 2020-06-08 https://github.com/nanoporetech/ont_fast5_api/ 3.1.3 ont-fast5-api 4.1.3 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 0 87 87 3051 3051 0 0 0 0 0 0 0 0 87 261 3051 9153
onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def ONTO-Toolkit is a collection of tools for managing ontologies. 2017-11-04 http://search.cpan.org/~easr/ONTO-PERL-1.45/ 1.45 perl-onto-perl 1.45 Up-to-date Ontology Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 0 68 69 582 663 0 0 0 0 0 0 0 0 68 205 582 1827
optdoe optdoe Optimal Design Of Experiment 2022-10-27 https://github.com/pablocarb/doebase v2.0.2 doebase To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
optitype optitype Precision HLA typing from NGS data 2021-02-17 https://github.com/FRED-2/OptiType 1.3.5 optitype 1.3.5 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 45 45 500 500 0 0 0 0 0 0 0 0 45 135 500 1500
orfipy orfipy Galaxy wrapper for ORFIPY 2022-04-07 https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy orfipy orfipy 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 99 99 897 897 239 239 1792 1792 0 0 0 0 338 1014 2689 8067
-orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy 2017-05-22 https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder 3.0.1b1 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder OrthoFinder OrthoFinder 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. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 419 419 2018 2018 0 0 0 0 58 58 438 438 477 1431 2456 7368
+orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy 2017-05-22 https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder 3.0.1b1 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder OrthoFinder OrthoFinder 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. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 419 419 2018 2018 0 0 0 0 58 58 438 438 477 1431 2456 7368
packaged_annotation_loader packaged_annotation_loader Tool to make cached genome annotation data available as a list of datasets collection 2022-01-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pacu pacu_map, pacu_snp PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 0.0.6 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing 2024-03-26 https://pairtools.readthedocs.io 1.1.0 pairtools 1.1.0 Up-to-date Sequence Analysis iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 196 196 14 14 19 19 0 0 0 0 30 90 215 645
-pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. 2021-03-06 https://github.com/cov-lineages/pangolin 4.3 pangolin 4.3.1 To update Sequence Analysis Tree-based sequence alignment, Variant classification Tree-based sequence alignment, Variant classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 508 508 7457 7457 377 377 8518 8518 259 259 2760 2760 1144 3432 18735 56205
+pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing 2024-03-26 https://pairtools.readthedocs.io 1.1.0 pairtools 1.1.2 To update Sequence Analysis iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 5 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 196 196 14 14 19 19 0 0 0 0 30 90 215 645
+pangolin pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. 2021-03-06 https://github.com/cov-lineages/pangolin 4.3 pangolin 4.3.1 To update Sequence Analysis Tree-based sequence alignment, Variant classification Tree-based sequence alignment, Variant classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 508 508 7457 7457 377 377 8518 8518 259 259 2760 2760 1144 3432 18735 56205
parse_mito_blast parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. 2022-05-12 https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py 1.0.2 parse_mito_blast 1.0.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 65 65 203 203 62 62 288 288 20 20 110 110 147 441 601 1803
-pathview pathview Pathview is a tool set for pathway based data integration and visualization. 2019-08-26 https://bioconductor.org/packages/release/bioc/html/pathview.html 1.34.0 bioconductor-pathview 1.42.0 To update Statistics, RNA, Micro-array Analysis Pathway or network analysis, Pathway or network visualisation Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1261 1261 6204 6211 1143 1143 6667 6667 189 189 1160 1160 2593 7779 14031 42100
+pathview pathview Pathview is a tool set for pathway based data integration and visualization. 2019-08-26 https://bioconductor.org/packages/release/bioc/html/pathview.html 1.34.0 bioconductor-pathview 1.42.0 To update Statistics, RNA, Micro-array Analysis Pathway or network analysis, Pathway or network visualisation Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1261 1261 6204 6211 1143 1143 6667 6667 189 189 1160 1160 2593 7779 14031 42100
pbgcpp pbgcpp Compute genomic consensus and call variants using PacBio reads mapped to a reference 2022-03-10 https://github.com/PacificBiosciences/gcpp 2.0.2 pbgcpp 2.0.2 Up-to-date Variant Analysis Variant calling Variant calling Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. 2022-03-10 https://github.com/PacificBiosciences/pbmm2 1.16.0 pbmm2 1.16.0 Up-to-date Next Gen Mappers Pairwise sequence alignment, Sorting Pairwise sequence alignment, Sorting Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 70 70 0 0 0 0 0 0 0 0 17 51 70 210
-pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. 2016-06-16 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram 1.0.2 openjdk To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 510 510 5505 5505 811 909 7932 8582 119 119 736 736 1440 4418 14173 43169
+pbmm2 pbmm2 A minimap2 SMRT wrapper for PacBio data. 2022-03-10 https://github.com/PacificBiosciences/pbmm2 1.16.0 pbmm2 1.16.99 To update Next Gen Mappers Pairwise sequence alignment, Sorting Pairwise sequence alignment, Sorting Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 70 70 0 0 0 0 0 0 0 0 17 51 70 210
+pe_histogram pe_histogram Contains a tool that produces an insert size histogram for a paired-end BAM file. 2016-06-16 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram 1.0.2 openjdk To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 510 510 5505 5505 811 909 7932 8582 119 119 736 736 1440 4418 14173 43169
peakzilla peakzilla Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. 2024-02-25 https://github.com/steinmann/peakzilla 1.0 python To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 18 18 0 0 0 0 0 0 0 0 9 27 18 54
-pear iuc_pear PEAR evaluates all possible paired-end read overlaps 2015-02-11 https://cme.h-its.org/exelixis/web/software/pear/ 0.9.6 pear 0.9.6 Up-to-date Fastq Manipulation Sequence merging Sequence merging Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 260 292 6269 6866 467 1664 5530 20068 198 300 5647 8471 925 4106 17446 70297
+pear iuc_pear PEAR evaluates all possible paired-end read overlaps 2015-02-11 https://cme.h-its.org/exelixis/web/software/pear/ 0.9.6 pear 0.9.6 Up-to-date Fastq Manipulation Sequence merging Sequence merging Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 260 292 6269 6866 467 1664 5530 20068 198 300 5647 8471 925 4106 17446 70297
pharokka pharokka rapid standardised annotation tool for bacteriophage genomes and metagenomes 2023-02-14 https://github.com/gbouras13/pharokka 1.3.2 "
pharokka
- " To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 334 334 5462 5462 0 0 0 0 52 52 309 309 386 1158 5771 17313
-phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.46.0 bioconductor-phyloseq 1.46.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. 4 1 4 4 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 193 193 1199 1199 0 0 0 0 1 1 6 6 194 582 1205 3615
-phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ 3.3.20220408 phyml 3.3.20220408 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 246 258 1975 2034 0 0 0 0 140 144 553 564 386 1174 2528 7654
-picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. 2017-01-11 http://broadinstitute.github.io/picard/ 3.1.1 picard 3.3.0 To update SAM Formatting Formatting Sequencing Sequencing devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard picard_samtofastq picard_samtofastq Create a FASTQ file. 31 31 31 31 0 0 0 0 0 0 0 0 0 0 31 4 31 0 0 0 0 0 0 31 0 0 0 0 0 0 31 31 31 0 11024 11956 386934 399039 32000 57111 366646 589980 2845 3398 56622 62258 45869 164203 810202 2671681
+ " To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 334 334 5462 5462 0 0 0 0 52 52 309 309 386 1158 5771 17313
+phyloseq phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.46.0 bioconductor-phyloseq 1.46.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. 4 1 4 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 193 193 1199 1199 0 0 0 0 1 1 6 6 194 582 1205 3615
+phyml phyml PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ 3.3.20220408 phyml 3.3.20220408 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 246 258 1975 2034 0 0 0 0 140 144 553 564 386 1174 2528 7654
+picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile Picard SAM/BAM manipulation tools. 2017-01-11 http://broadinstitute.github.io/picard/ 3.1.1 picard 3.3.0 To update SAM Formatting Formatting Sequencing Sequencing devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard picard_samtofastq picard_samtofastq Create a FASTQ file. 31 31 31 0 0 0 0 0 0 0 0 0 0 0 0 31 4 31 0 0 0 0 0 31 0 0 0 0 0 0 31 31 31 0 11024 11956 386934 399039 32000 57111 366646 589980 2845 3398 56622 62258 45869 164203 810202 2671681
pick_value pick_value Compose a text parameter value using text, integer and float values 2023-01-23 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 41 41 1607 1607 53 53 490 490 4 4 127 127 98 294 2224 6672
-picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust picrust PICRUSt 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. 0 6 5 6 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 144 165 867 1128 0 0 0 0 121 121 2106 2106 265 816 2973 9180
+picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust picrust PICRUSt 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. 0 6 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 144 165 867 1128 0 0 0 0 121 121 2106 2106 265 816 2973 9180
picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2021-07-09 https://github.com/picrust/picrust2/wiki 2.5.3 picrust2 2.5.3 Up-to-date Metagenomics Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. 0 7 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 382 382 2532 2532 1 1 1 1 83 83 1311 1311 466 1398 3844 11532
-pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria 2016-08-11 https://github.com/broadinstitute/pilon/wiki 1.20.1 pilon 1.24 To update Variant Analysis Sequence assembly, Analysis, Read alignment Sequence assembly, Analysis Assembly Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1115 1144 9045 9458 1070 1070 7989 7989 726 741 3945 4137 2911 8777 20979 63542
-pipelign pipelign Multipe sequence alignment 2019-08-20 https://github.com/asmmhossain/pipelign/ 0.2 pipelign 0.2 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 231 231 1245 1245 630 630 9046 9046 0 0 0 0 861 2583 10291 30873
-plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow 1.1.0 plasflow 1.1.0 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 711 734 37086 37272 583 583 6346 6346 61 61 3065 3065 1355 4088 46497 139677
-plasmidfinder plasmidfinder """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""" 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 251 251 14652 14652 0 0 0 0 18 18 101 101 269 807 14753 44259
-plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2020-09-14 https://www.cog-genomics.org/plink 1.90b6.21 plink 1.90b6.21 Up-to-date Genome-Wide Association Study Genetic variation analysis Genetic variation analysis GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 127 851 851 43 43 249 249 0 0 0 0 170 510 1100 3300
-polypolish polypolish """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.""" 2022-09-22 https://github.com/rrwick/Polypolish 0.6.0 polypolish 0.6.0 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish Polypolish Polypolish 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. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 86 86 731 731 0 0 0 0 4 4 42 42 90 270 773 2319
-porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads 2018-09-13 https://github.com/rrwick/Porechop porechop 0.2.4 To update Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2627 2711 262015 262852 1918 1918 83623 83623 1037 1037 52558 52558 5582 16830 398196 1195425
+pilon pilon pilon is a tool for assembly improvement and variant analysis in bacteria 2016-08-11 https://github.com/broadinstitute/pilon/wiki 1.20.1 pilon 1.24 To update Variant Analysis Sequence assembly, Analysis, Read alignment Sequence assembly, Analysis Assembly Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1115 1144 9045 9458 1070 1070 7989 7989 726 741 3945 4137 2911 8777 20979 63542
+pipelign pipelign Multipe sequence alignment 2019-08-20 https://github.com/asmmhossain/pipelign/ 0.2 pipelign 0.2 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 231 231 1245 1245 630 630 9046 9046 0 0 0 0 861 2583 10291 30873
+plasflow PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow 1.1.0 plasflow 1.1.0 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 711 734 37086 37272 583 583 6346 6346 61 61 3065 3065 1355 4088 46497 139677
+plasmidfinder plasmidfinder """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""" 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 251 251 14652 14652 0 0 0 0 18 18 101 101 269 807 14753 44259
+plink plink Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2020-09-14 https://www.cog-genomics.org/plink 1.90b6.21 plink 1.90b6.21 Up-to-date Genome-Wide Association Study Genetic variation analysis Genetic variation analysis GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 127 127 851 851 43 43 249 249 0 0 0 0 170 510 1100 3300
+polypolish polypolish """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.""" 2022-09-22 https://github.com/rrwick/Polypolish 0.6.0 polypolish 0.6.0 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish Polypolish Polypolish 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. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 86 86 731 731 0 0 0 0 4 4 42 42 90 270 773 2319
+porechop porechop Porechop - Finding and removing adapters from Oxford Nanopore reads 2018-09-13 https://github.com/rrwick/Porechop porechop 0.2.4 To update Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2627 2711 262015 262852 1918 1918 83623 83623 1037 1037 52558 52558 5582 16830 398196 1195425
presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. 2017-08-30 https://presto.readthedocs.io/ 0.6.2 presto 0.7.2 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequencing, DNA, Immunology Sequencing, DNA, Immunology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1392 1599 63244 65177 0 0 0 0 1392 4383 63244 191665
-prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION+galaxy2 prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 253 281 10152 10626 1240 1240 10581 10581 0 0 0 0 1493 4507 20733 62673
-prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal 2.6.3 prodigal 2.6.3 Up-to-date Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 167 167 1902 1902 0 0 0 0 0 0 0 0 167 501 1902 5706
-progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 2015-05-15 http://darlinglab.org/mauve/user-guide/progressivemauve.html progressivemauve snapshot_2015_02_13 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 678 695 2064 2173 1034 1034 2900 2900 0 0 0 0 1712 5153 4964 15001
-prokka prokka Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka 1.14.6 prokka 1.14.6 Up-to-date Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 7475 7721 464359 476554 11243 12384 313285 331256 4358 4947 131211 141875 23076 71204 908855 2767395
+prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION+galaxy2 prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 253 281 10152 10626 1240 1240 10581 10581 0 0 0 0 1493 4507 20733 62673
+prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal 2.6.3 prodigal 2.6.3 Up-to-date Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 167 167 1902 1902 0 0 0 0 0 0 0 0 167 501 1902 5706
+progressivemauve progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 2015-05-15 http://darlinglab.org/mauve/user-guide/progressivemauve.html progressivemauve snapshot_2015_02_13 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 678 695 2064 2173 1034 1034 2900 2900 0 0 0 0 1712 5153 4964 15001
+prokka prokka Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka 1.14.6 prokka 1.14.6 Up-to-date Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 7475 7721 464359 476554 11243 12384 313285 331256 4358 4947 131211 141875 23076 71204 908855 2767395
prot_scriber prot_scriber Protein annotation of short human readable descriptions 2022-05-10 https://github.com/usadellab/prot-scriber 0.1.6 prot-scriber 0.1.6 Up-to-date Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 7 7 10 10 0 0 0 0 0 0 0 0 7 21 10 30
-proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. 2020-02-05 https://gitlab.com/paulklemm_PHD/proteinortho 6.3.1 proteinortho 6.3.3 To update Proteomics Sequence clustering, Sequence analysis Sequence clustering, Sequence analysis Comparative genomics Comparative genomics iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 501 501 3962 3962 0 0 0 0 0 0 0 0 501 1503 3962 11886
+proteinortho proteinortho, proteinortho_grab_proteins, proteinortho_summary Proteinortho is a tool to detect orthologous proteins/genes within different species. 2020-02-05 https://gitlab.com/paulklemm_PHD/proteinortho 6.3.4 proteinortho 6.3.4 Up-to-date Proteomics Sequence clustering, Sequence analysis Sequence clustering, Sequence analysis Comparative genomics Comparative genomics iuc https://gitlab.com/paulklemm_PHD/proteinortho https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 501 501 3962 3962 0 0 0 0 0 0 0 0 501 1503 3962 11886
psiclass psiclass PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. 2023-09-06 https://github.com/splicebox/PsiCLASS 1.0.3 psiclass 1.0.3 Up-to-date Transcriptomics Transcriptome assembly Transcriptome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 5 5 24 24 0 0 0 0 0 0 0 0 5 15 24 72
pureclip pureclip PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data 2018-04-26 https://github.com/skrakau/PureCLIP 1.0.4 pureclip 1.3.1 To update Sequence Analysis, RNA, CLIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 81 92 1319 1507 0 0 0 0 0 0 0 0 81 254 1319 4145
purge_dups purge_dups Purge haplotigs and overlaps in an assembly based on read depth 2021-02-03 https://github.com/dfguan/purge_dups 1.2.6 purge_dups 1.2.6 Up-to-date Assembly Genome assembly, Read binning, Scaffolding Genome assembly, Read binning, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 287 287 17782 17782 65 65 853 853 65 65 2224 2224 417 1251 20859 62577
-pycoqc pycoqc QC metrics for ONT Basecalling 2021-03-02 https://github.com/tleonardi/pycoQC 2.5.2 pycoqc 2.5.2 Up-to-date Nanopore Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Sequence analysis, Data quality management, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 557 557 22742 22742 716 716 2159 2159 448 448 776 776 1721 5163 25677 77031
-pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. 2018-06-08 https://github.com/deeptools/pyGenomeTracks 3.8 pygenometracks 3.9 To update Visualization Visualisation, Formatting Visualisation, Formatting Model organisms, Imaging, Workflows Model organisms, Imaging, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks pygenometracks pyGenomeTracks 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:. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 986 996 12858 13232 943 943 8092 8092 124 124 3238 3238 2053 6169 24188 72938
-pysradb_search pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. 2022-11-10 https://github.com/saketkc/pysradb 1.4.2 pysradb 2.2.2 To update Sequence Analysis Deposition, Data retrieval Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics Sequencing, Gene transcripts, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 35 35 163 163 0 0 0 0 0 0 0 0 35 105 163 489
+pycoqc pycoqc QC metrics for ONT Basecalling 2021-03-02 https://github.com/tleonardi/pycoQC 2.5.2 pycoqc 2.5.2 Up-to-date Nanopore Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Sequence analysis, Data quality management, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 557 557 22742 22742 716 716 2159 2159 448 448 776 776 1721 5163 25677 77031
+pygenometracks pygenomeTracks pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. 2018-06-08 https://github.com/deeptools/pyGenomeTracks 3.8 pygenometracks 3.9 To update Visualization Visualisation, Formatting Visualisation, Formatting Model organisms, Imaging, Workflows Model organisms, Imaging, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks pygenometracks pyGenomeTracks 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:. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 986 996 12858 13232 943 943 8092 8092 124 124 3238 3238 2053 6169 24188 72938
+pysradb_search pysradb_search pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. 2022-11-10 https://github.com/saketkc/pysradb 1.4.2 pysradb 2.2.2 To update Sequence Analysis Deposition, Data retrieval Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics Sequencing, Gene transcripts, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 35 35 163 163 0 0 0 0 0 0 0 0 35 105 163 489
qfilt qfilt Filter sequencing data 2018-06-06 https://github.com/veg/qfilt 1.0.0+galaxy1 qfilt 0.0.1 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-qiime 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 QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 32 32 0 0 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 3375 3785 31825 34677 1 1 1 1 4 4 14 14 3380 10550 31840 98372
-qiime qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 209 238 2092 2342 0 0 0 0 1 1 2 2 210 659 2094 6532
+qiime qiime_collapse_samples, qiime_make_otu_table QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 209 238 2092 2342 0 0 0 0 1 1 2 2 210 659 2094 6532
+qiime 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 QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 0 0 32 0 0 0 0 0 0 0 0 0 0 0 0 31 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 0 3375 3785 31825 34677 1 1 1 1 4 4 14 14 3380 10550 31840 98372
qiime_extract_viz qiime_extract_viz Extract vizualization from QIIME artifacts 2022-10-06 http://www.qiime.org 0.1.0 unzip To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 17 17 0 0 0 0 0 0 0 0 8 24 17 51
-qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq 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. 2019-10-10 http://qualimap.bioinfo.cipf.es/ 2.3 qualimap 2.3 Up-to-date Sequence Analysis, Transcriptomics, SAM Sequencing quality control Sequencing quality control Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap qualimap QualiMap 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. 4 4 4 1 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 0 0 0 0 1 0 0 0 0 0 0 4 4 4 0 3239 3239 684820 684820 3881 3881 90503 90503 826 826 29018 29018 7946 23838 804341 2413023
-quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. 2016-09-07 http://quast.bioinf.spbau.ru/ 5.3.0 quast 5.3.0 Up-to-date Assembly Visualisation, Sequence assembly validation Visualisation, Sequence assembly validation Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 7787 7971 67737 69738 9692 10646 51925 56602 3890 4127 32003 34145 21369 65482 151665 463815
+qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq 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. 2019-10-10 http://qualimap.bioinfo.cipf.es/ 2.3 qualimap 2.3 Up-to-date Sequence Analysis, Transcriptomics, SAM Sequencing quality control Sequencing quality control Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap qualimap QualiMap 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. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 0 0 0 1 0 0 0 0 0 0 4 4 4 0 3239 3239 684820 684820 3881 3881 90503 90503 826 826 29018 29018 7946 23838 804341 2413023
+quast quast Quast (Quality ASsessment Tool) evaluates genome assemblies. 2016-09-07 http://quast.bioinf.spbau.ru/ 5.3.0 quast 5.3.0 Up-to-date Assembly Visualisation, Sequence assembly validation Visualisation, Sequence assembly validation Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 7787 7971 67737 69738 9692 10646 51925 56602 3890 4127 32003 34145 21369 65482 151665 463815
query_impc query_impc Contains a tool to query the IMPC database. 2023-10-11 https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests To update Convert Formats, Web Services iuc https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 3 3 0 0 0 0 0 0 0 0 2 6 3 9
quickmerge quickmerge Merge long-read and hybrid assemblies to increase contiguity 2022-07-08 https://github.com/mahulchak/quickmerge 0.3 quickmerge 0.3 Up-to-date Assembly Genome assembly, Scaffolding, De-novo assembly, Genotyping Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge quickmerge quickmerge 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. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-quicktree quicktree neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree 2.5 quicktree 2.5 Up-to-date Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-ragtag ragtag Reference-guided scaffolding of draft genomes tool. 2021-11-10 https://github.com/malonge/RagTag 2.1.0 ragtag 2.1.0 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 480 480 4844 4844 0 0 0 0 3 3 7 7 483 1449 4851 14553
-rapidnj rapidnj Galaxy wrapper for the RapidNJ tool 2020-05-11 https://birc.au.dk/software/rapidnj/ 2.3.2 rapidnj 2.3.2 Up-to-date Phylogenetics Phylogenetic tree generation Phylogeny Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 339 339 256 256 1737 1737 1 1 6 6 287 861 2082 6246
+quicktree quicktree neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree 2.5 quicktree 2.5 Up-to-date Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ragtag ragtag Reference-guided scaffolding of draft genomes tool. 2021-11-10 https://github.com/malonge/RagTag 2.1.0 ragtag 2.1.0 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 480 480 4844 4844 0 0 0 0 3 3 7 7 483 1449 4851 14553
+rapidnj rapidnj Galaxy wrapper for the RapidNJ tool 2020-05-11 https://birc.au.dk/software/rapidnj/ 2.3.2 rapidnj 2.3.2 Up-to-date Phylogenetics Phylogenetic tree generation Phylogeny Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 30 30 339 339 256 256 1737 1737 1 1 6 6 287 861 2082 6246
rasusa rasusa Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa 2.0.0 rasusa 2.1.0 To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 42 42 0 0 0 0 0 0 0 0 9 27 42 126
-raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ 8.2.12 raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 966 966 10905 10905 587 587 5100 5114 765 892 4955 6094 2318 7081 20960 64033
+raxml raxml RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ 8.2.12 raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 966 966 10905 10905 587 587 5100 5114 765 892 4955 6094 2318 7081 20960 64033
rcorrector rcorrector Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. 2018-05-02 https://github.com/mourisl/Rcorrector 1.0.3+galaxy1 rcorrector 1.0.7 To update Fastq Manipulation Sequencing error detection Sequencing error detection RNA, RNA-Seq, Sequencing RNA, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 57 57 655 655 0 0 0 0 0 0 0 0 57 171 655 1965
-read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 80 80 3710 3710 6 6 7 7 0 0 0 0 86 258 3717 11151
-recentrifuge recentrifuge """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.""" 2022-05-04 https://github.com/khyox/recentrifuge 1.15.0 recentrifuge 1.15.0 Up-to-date Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 472 472 13 13 32 32 4 4 6 6 109 327 510 1530
-red red Red (REpeat Detector) 2022-09-14 https://github.com/BioinformaticsToolsmith/Red 2018.09.10 red 2018.09.10 Up-to-date Sequence Analysis RNA-Seq analysis, Editing RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation RNA, Sequencing, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 859 859 142 142 305 305 58 58 227 227 403 1209 1391 4173
-repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2018-04-21 http://www.repeatmasker.org/ 4.1.5 repeatmasker 4.0.9_p2 To update Sequence Analysis Genome annotation Genome annotation Sequence analysis, Sequence composition, complexity and repeats Sequence composition, complexity and repeats bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 810 810 5998 5998 803 803 7618 7618 292 292 3135 3135 1905 5715 16751 50253
-repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA 2021-08-26 https://www.repeatmasker.org/RepeatModeler/ 2.0.5 To update Genome annotation Repeat sequence detection Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats Sequence composition, complexity and repeats, Sequence composition, complexity and repeats csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 413 413 7963 7963 220 220 1485 1485 168 168 8402 8402 801 2403 17850 53550
+read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep 0.2.2 read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 80 80 3710 3710 6 6 7 7 0 0 0 0 86 258 3717 11151
+recentrifuge recentrifuge """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.""" 2022-05-04 https://github.com/khyox/recentrifuge 1.15.0 recentrifuge 1.15.0 Up-to-date Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 92 92 472 472 13 13 32 32 4 4 6 6 109 327 510 1530
+red red Red (REpeat Detector) 2022-09-14 https://github.com/BioinformaticsToolsmith/Red 2018.09.10 red 2018.09.10 Up-to-date Sequence Analysis RNA-Seq analysis, Editing RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation RNA, Sequencing, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 203 203 859 859 142 142 305 305 58 58 227 227 403 1209 1391 4173
+repeat_masker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2018-04-21 http://www.repeatmasker.org/ 4.1.5 repeatmasker 4.0.9_p2 To update Sequence Analysis Genome annotation Genome annotation Sequence analysis, Sequence composition, complexity and repeats Sequence composition, complexity and repeats bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 810 810 5998 5998 803 803 7618 7618 292 292 3135 3135 1905 5715 16751 50253
+repeatmodeler repeatmodeler RepeatModeler - Model repetitive DNA 2021-08-26 https://www.repeatmasker.org/RepeatModeler/ 2.0.5 To update Genome annotation Repeat sequence detection Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats Sequence composition, complexity and repeats, Sequence composition, complexity and repeats csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 413 413 7963 7963 220 220 1485 1485 168 168 8402 8402 801 2403 17850 53550
repmatch_gff3 repmatch_gff3 Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. 2015-12-18 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 219 415 721 0 0 0 0 128 475 415 1551
resize_coordinate_window resize_coordinate_window Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. 2016-01-13 1.0.2 python To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 8 9 75 86 30 57 138 216 0 0 0 0 38 142 213 728
revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers 2024-03-19 https://gitlab.com/Bernt/revoluzer/ 0.1.6 revoluzer 0.1.6 Up-to-date Phylogenetics Structural variation detection Structural variation detection Molecular evolution, Phylogeny Molecular evolution, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 52 2444 2444 0 0 0 0 0 0 0 0 52 156 2444 7332
rgcca rgcca multi-block analysis 2020-09-02 https://github.com/rgcca-factory/RGCCA 3.0.2 rgccacmd 3.0.3 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 44 44 35 35 77 77 0 0 0 0 41 123 121 363
-rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper 2015-05-18 https://github.com/alexdobin/STAR 2.7.11a star 2.7.11b To update Next Gen Mappers, Transcriptomics, Single Cell Sequence alignment Sequence alignment RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar star STAR Ultrafast universal RNA-seq data aligner 2 2 2 2 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 2 0 0 0 0 0 1 2 2 2 0 10142 10900 438078 473957 15284 18791 325474 403925 1359 1449 49662 53138 26785 84710 813214 2557448
-rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. 2020-10-05 https://github.com/ablab/rnaquast 2.3.0 rnaquast 2.3.0 Up-to-date Assembly, RNA De-novo assembly, Transcriptome assembly, Sequence assembly validation De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-Seq Sequence assembly, Transcriptomics, RNA-Seq iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 254 254 1522 1522 75 75 372 372 1 1 5 5 330 990 1899 5697
-roary roary Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ 3.13.0 roary 3.13.0 Up-to-date Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary roary Roary 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1459 1501 15196 15685 1768 1768 12188 12188 518 555 4881 5539 3745 11314 32265 97942
+rgrnastar rna_star, rna_starsolo RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper 2015-05-18 https://github.com/alexdobin/STAR 2.7.11a star 2.7.11b To update Next Gen Mappers, Transcriptomics, Single Cell Sequence alignment Sequence alignment RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar star STAR Ultrafast universal RNA-seq data aligner 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 2 0 0 0 0 0 1 2 2 2 0 10142 10900 438078 473957 15284 18791 325474 403925 1359 1449 49662 53138 26785 84710 813214 2557448
+rnaquast rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. 2020-10-05 https://github.com/ablab/rnaquast 2.3.0 rnaquast 2.3.0 Up-to-date Assembly, RNA De-novo assembly, Transcriptome assembly, Sequence assembly validation De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-Seq Sequence assembly, Transcriptomics, RNA-Seq iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 254 254 1522 1522 75 75 372 372 1 1 5 5 330 990 1899 5697
+roary roary Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ 3.13.0 roary 3.13.0 Up-to-date Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary roary Roary 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1459 1501 15196 15685 1768 1768 12188 12188 518 555 4881 5539 3745 11314 32265 97942
rp2biosensor rp2biosensor Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output 2023-01-05 https://github.com/brsynth/rp2biosensor 3.2.1 rp2biosensor To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rp2paths rp2paths Enumerate and seperate the different pathways generated by RetroPath2.0 2022-10-17 https://github.com/brsynth/rp2paths 1.5.1 rp2paths To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rpbasicdesign rpbasicdesign Extracting enzyme IDs from rpSBML files 2022-03-30 https://github.com/brsynth/rpbasicdesign 1.2.2 rpbasicdesign To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rpfba rpfba Perform FBA for the RetroPath2.0 heterologous pathways 2022-01-17 https://github.com/brsynth/rptools/releases 5.12.3 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz Suite of tools that work on rpSBML format 2022-11-16 https://github.com/brsynth/rptools 5.13.1 rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
rrparser rrparser Reaction Rules Parser 2022-06-27 https://github.com/brsynth/RRParser 2.5.2 rrparser To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-rseqc 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 an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc rseqc RSeQC 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. 22 22 22 22 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 22 22 22 0 8341 9385 136315 147595 10696 12789 138707 161046 1593 1695 22718 23767 20630 65129 297740 927888
+rseqc 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 an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc rseqc RSeQC 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. 22 22 22 0 0 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 22 0 0 0 0 0 0 22 22 22 0 8341 9385 136315 147595 10696 12789 138707 161046 1593 1695 22718 23767 20630 65129 297740 927888
ruvseq ruvseq Remove Unwanted Variation from RNA-Seq Data 2018-08-30 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 1.26.0 bioconductor-ruvseq 1.36.0 To update Transcriptomics, RNA, Statistics Differential gene expression analysis Differential gene expression analysis Gene expression, RNA-seq Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 178 193 1286 1364 299 299 2220 2220 0 0 0 0 477 1446 3506 10596
-salsa salsa A tool to scaffold long read assemblies with Hi-C 2021-01-14 https://github.com/marbl/SALSA 2.3 salsa2 2.3 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Sequence assembly, DNA binding sites, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 119 119 463 463 87 87 1038 1038 24 24 410 410 230 690 1911 5733
+salsa salsa A tool to scaffold long read assemblies with Hi-C 2021-01-14 https://github.com/marbl/SALSA 2.3 salsa2 2.3 Up-to-date Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Sequence assembly, DNA binding sites, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 119 119 463 463 87 87 1038 1038 24 24 410 410 230 690 1911 5733
samblaster samblaster samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files 2016-12-18 https://github.com/GregoryFaust/samblaster 0.1.26 samblaster 0.1.26 Up-to-date SAM, Fastq Manipulation, Variant Analysis Split read mapping Split read mapping DNA, Sequencing, Mapping DNA, Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sansa sansa_annotate Sansa is a tool for structural variant annotation. 2020-12-05 https://github.com/dellytools/sansa 0.2.2 sansa 0.2.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 36 36 138 138 0 0 0 0 0 0 0 0 36 108 138 414
sarscov2formatter sarscov2formatter sarscov2formatter custom script 2020-05-01 https://github.com/nickeener/sarscov2formatter 1.0 sarscov2formatter 1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 16 174 174 29 29 399 399 0 0 0 0 45 135 573 1719
@@ -981,95 +983,95 @@ scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_no
sceasy_convert sceasy_convert Converter between difference single-cell formats 2023-11-10 https://github.com/cellgeni/sceasy/ 0.0.7 r-sceasy 0.0.7 Up-to-date Single Cell, Spatial Omics, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy sceasy sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 222 222 1059 1059 71 71 426 426 1 1 1 1 294 882 1486 4458
schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. 2019-12-16 https://github.com/joachimwolff/schicexplorer 4 schicexplorer 7 To update Sequence Analysis, Transcriptomics, Visualization, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer 16 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 16 0 78 78 809 809 2 2 3 3 16 16 105 105 96 288 917 2751
scikit_bio scikit_bio_diversity_beta_diversity scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics 2016-05-31 http://scikit-bio.org/ 0.4.2 scikit-bio 0.4.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 283 402 1503 1955 0 0 0 0 284 971 1504 4964
-scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary 1.6.16 scoary 1.6.16 Up-to-date Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary scoary Scoary 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 90 90 901 901 0 0 0 0 0 0 0 0 90 270 901 2703
+scoary scoary Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary 1.6.16 scoary 1.6.16 Up-to-date Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary scoary Scoary 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. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 90 90 901 901 0 0 0 0 0 0 0 0 90 270 901 2703
scpipe scpipe A flexible preprocessing pipeline for single-cell RNA-sequencing data 2018-08-12 http://bioconductor.org/packages/release/bioc/html/scPipe.html 1.0.0+galaxy2 bioconductor-scpipe 2.2.0 To update Transcriptomics, Single Cell Genome annotation, Validation, Alignment, Visualisation Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing Gene expression, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 34 38 284 632 61 61 786 786 1 1 1 1 96 292 1071 3561
seacr seacr SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. 2020-02-05 https://github.com/FredHutch/SEACR 1.3 seacr 1.3 Up-to-date Epigenetics, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 116 116 5106 5106 241 241 6419 6419 0 0 0 0 357 1071 11525 34575
selenzy_wrapper selenzy_wrapper Performs enzyme selection from a reaction query. 2022-06-29 https://github.com/brsynth/selenzy-wrapper 0.3.0 selenzy_wrapper 0.3.0 Up-to-date Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.0.2 semibin 2.1.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 0 0 6 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 93 93 931 931 0 0 0 0 0 0 0 0 93 279 931 2793
+semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.0.2 semibin 2.1.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 93 93 931 931 0 0 0 0 0 0 0 0 93 279 931 2793
seq2hla seq2hla Precision HLA typing and expression from RNAseq data 2020-02-20 https://github.com/TRON-Bioinformatics/seq2HLA 2.3 seq2hla 2.3 Up-to-date Sequence Analysis Read mapping, Genetic variation analysis Read mapping, Genetic variation analysis Transcriptomics, Mapping Transcriptomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 40 342 342 0 0 0 0 0 0 0 0 40 120 342 1026
-seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.9.0 seqkit 2.9.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit seqkit seqkit 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. 0 2 5 3 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 247 247 3364 3364 0 0 0 0 33 33 244 244 280 840 3608 10824
+seqkit seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.9.0 seqkit 2.9.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit seqkit seqkit 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. 0 2 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 247 247 3364 3364 0 0 0 0 33 33 244 244 280 840 3608 10824
seqprep seqprep Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 102 102 2424 2424 0 0 0 0 0 0 0 0 102 306 2424 7272
seqsero2 seqsero2 Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.1 seqsero2 1.3.1 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 seqsero2 SeqSero2 "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)" 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 42 4182 4182 0 0 0 0 0 0 0 0 42 126 4182 12546
-seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats 2015-01-13 https://github.com/lh3/seqtk 1.4 seqtk 1.4 Up-to-date Sequence Analysis Data handling, Sequence file editing Data handling, Sequence file editing Data management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. 15 15 15 15 0 0 0 0 0 0 0 0 0 0 14 0 14 0 0 0 0 0 0 15 0 0 0 0 0 0 14 14 14 14 2210 2300 72816 73514 2313 2669 102777 107831 682 682 154613 154613 5205 16061 330206 996370
-seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics 2018-08-20 https://satijalab.org/seurat/ 5.0 r-seurat 3.0.2 To update Single Cell, Transcriptomics, Sequence Analysis RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat seurat Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 1 1 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 11 11 121 121 5 5 32 32 0 0 0 0 16 48 153 459
+seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq Toolkit for processing sequences in FASTA/Q formats 2015-01-13 https://github.com/lh3/seqtk 1.4 seqtk 1.4 Up-to-date Sequence Analysis Data handling, Sequence file editing Data handling, Sequence file editing Data management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. 15 15 15 0 0 0 0 0 0 0 0 0 0 0 0 14 0 14 0 0 0 0 0 15 0 0 0 0 0 0 14 14 14 14 2210 2300 72816 73514 2313 2669 102777 107831 682 682 154613 154613 5205 16061 330206 996370
+seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics 2018-08-20 https://satijalab.org/seurat/ 5.0 r-seurat 3.0.2 To update Single Cell, Transcriptomics, Sequence Analysis RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat seurat Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 1 1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 11 11 121 121 5 5 32 32 0 0 0 0 16 48 153 459
sfold sfold Predict the probable RNA secondary structures through structure ensemble sampling 2024-10-09 https://github.com/Ding-RNA-Lab/Sfold 2.2.0 To update RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sfold https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-shasta shasta Fast de novo assembly of long read sequencing data 2020-11-11 https://github.com/chanzuckerberg/shasta 0.6.0 shasta 0.13.0 To update Assembly, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 308 308 913 913 0 0 0 0 73 73 568 568 381 1143 1481 4443
-shorah_amplicon shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode 2018-11-27 https://github.com/cbg-ethz/shorah/blob/master/README.md 1.1.3 shorah 1.99.2 To update Sequence Analysis Haplotype mapping, Variant calling Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Metagenomics, Sequencing, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah shorah ShoRAH 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. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-shovill shovill Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill 1.1.0 shovill 1.1.0 Up-to-date Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill shovill shovill 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2273 2356 46125 47376 3971 3971 40577 40577 1085 1199 19960 21130 7329 22184 106662 322407
-sickle sickle A windowed adaptive trimming tool for FASTQ files using quality 2015-11-03 https://github.com/najoshi/sickle 1.33.2 sickle-trim 1.33 To update Fastq Manipulation, Sequence Analysis Sequence trimming Sequence trimming Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 555 608 18184 18937 1063 1063 10514 10514 0 0 0 0 1618 4907 28698 86847
+shasta shasta Fast de novo assembly of long read sequencing data 2020-11-11 https://github.com/chanzuckerberg/shasta 0.6.0 shasta 0.13.0 To update Assembly, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 308 308 913 913 0 0 0 0 73 73 568 568 381 1143 1481 4443
+shorah_amplicon shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode 2018-11-27 https://github.com/cbg-ethz/shorah/blob/master/README.md 1.1.3 shorah 1.99.2 To update Sequence Analysis Haplotype mapping, Variant calling Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Metagenomics, Sequencing, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah shorah ShoRAH 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. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+shovill shovill Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill 1.1.0 shovill 1.1.0 Up-to-date Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill shovill shovill 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2273 2356 46125 47376 3971 3971 40577 40577 1085 1199 19960 21130 7329 22184 106662 322407
+sickle sickle A windowed adaptive trimming tool for FASTQ files using quality 2015-11-03 https://github.com/najoshi/sickle 1.33.2 sickle-trim 1.33 To update Fastq Manipulation, Sequence Analysis Sequence trimming Sequence trimming Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 0 555 608 18184 18937 1063 1063 10514 10514 0 0 0 0 1618 4907 28698 86847
simpleweather simple_weather provides simple weather in text format 2016-07-19 http://wttr.in/ 0.1.2 curl To update Visualization, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix A text mining framework for interactive analysis and visualization of similarities among biomedical entities. 2021-02-28 https://github.com/dlal-group/simtext 0.0.2 r-argparse 1.0.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tools/simtext https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 68 68 220 220 0 0 0 0 10 10 416 416 78 234 636 1908
-sina sina SINA reference based multiple sequence alignment 2019-10-11 https://sina.readthedocs.io/en/latest/ 1.7.2 sina 1.7.2 Up-to-date Sequence Analysis Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 125 125 1369 1369 420 420 2398 2398 0 0 0 0 545 1635 3767 11301
+sina sina SINA reference based multiple sequence alignment 2019-10-11 https://sina.readthedocs.io/en/latest/ 1.7.2 sina 1.7.2 Up-to-date Sequence Analysis Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 125 125 1369 1369 420 420 2398 2398 0 0 0 0 545 1635 3767 11301
slamdunk alleyoop, slamdunk Slamdunk maps and quantifies SLAMseq reads 2018-10-05 http://t-neumann.github.io/slamdunk 0.4.3 slamdunk 0.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 16 16 346 362 67 67 872 872 0 0 0 0 83 249 1218 3670
sleuth sleuth Sleuth is a program for differential analysis of RNA-Seq data. 2023-05-30 https://github.com/pachterlab/sleuth 0.30.1 r-sleuth 0.30.1 Up-to-date Transcriptomics, RNA, Statistics Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-Seq, Gene expression, Statistics and probability RNA-Seq, Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 26 26 141 141 0 0 0 0 0 0 0 0 26 78 141 423
smallgenomeutilities smgu_frameshift_deletions_checks Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.4.1 smallgenomeutilities 0.4.1 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 158 158 0 0 0 0 0 0 0 0 8 24 158 474
smudgeplot smudgeplot Inference of ploidy and heterozygosity structure using whole genome sequencing 2022-06-30 https://github.com/KamilSJaron/smudgeplot 0.2.5 smudgeplot 0.4.0 To update Assembly Sequence trimming, Genotyping, k-mer counting Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Sequence assembly, Genetic variation, Mathematics galaxy-australia https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 61 61 325 325 54 54 137 137 63 63 843 843 178 534 1305 3915
snap snap, snap_training SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 331 358 1499 1638 244 244 779 779 83 83 467 467 658 2001 2745 8374
snapatac2 snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis 2024-05-16 https://kzhang.org/SnapATAC2/ 2.6.4 To update Single Cell, Epigenetics Essential dynamics, Dimensionality reduction, Gene expression profiling Essential dynamics, Dimensionality reduction, Gene expression profiling Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 snapatac SnapATAC SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets. 4 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 14 1817 1817 2 2 4 4 4 4 136 136 20 60 1957 5871
-sniffles sniffles Galaxy wrapper for sniffles 2020-08-29 https://github.com/fritzsedlazeck/Sniffles 2.5.2 sniffles 2.5.2 Up-to-date Sequence Analysis Sequence analysis, Structural variation detection Sequence analysis, Structural variation detection DNA structural variation, Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 134 1141 1141 156 156 606 606 80 80 2267 2267 370 1110 4014 12042
-snipit snipit Summarise snps relative to a reference sequence 2022-07-17 https://github.com/aineniamh/snipit 1.6 snipit 1.6 Up-to-date Variant Analysis, Sequence Analysis Base position variability plotting Base position variability plotting Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit snipit snipit Summarise snps relative to a reference sequence 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 905 905 0 0 0 0 0 0 0 0 44 132 905 2715
-snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 3448 3602 121363 124773 3945 3945 92504 92504 2705 3073 48068 52034 10098 30816 261935 793181
-snp_dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment 2019-10-18 https://github.com/tseemann/snp-dists 0.8.2 snp-dists 0.8.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 807 807 6555 6555 171 171 5336 5336 182 182 1143 1143 1160 3480 13034 39102
-snp_sites snp_sites Finds SNP sites from a multi-FASTA alignment file 2017-06-28 https://github.com/sanger-pathogens/snp-sites 2.5.1 snp-sites 2.5.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 663 663 6597 6597 256 256 1467 1467 114 114 1279 1279 1033 3099 9343 28029
-snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox 2014-11-11 http://snpeff.sourceforge.net/ 5.2 biopython 1.70 To update Genome-Wide Association Study, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff 5 5 5 5 0 0 0 0 0 0 1 0 0 0 0 5 5 0 0 0 0 0 0 5 0 0 0 0 0 0 5 5 5 0 7181 7908 103826 108296 15871 22769 115727 178110 2148 2321 11817 13155 25200 83398 231370 762301
-snpeff_sars_cov_2 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox 2020-06-17 http://snpeff.sourceforge.net/ To update Genome-Wide Association Study, Variant Analysis SNP detection SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs DNA polymorphism, Nucleic acid sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1276 1276 764895 764895 1636 1636 94572 94572 561 561 26990 26990 3473 10419 886457 2659371
-snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region 2020-12-02 https://github.com/BrownfieldPlantLab/SNPFreqPlot 1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 338 338 3683 3683 433 433 1401 1401 95 95 1029 1029 866 2598 6113 18339
-snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift 8 8 8 8 0 0 0 0 0 0 8 0 0 0 0 0 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 3602 4283 5142904 5146618 7013 9678 382391 421190 960 1184 104030 105024 11575 38295 5629325 16931482
+sniffles sniffles Galaxy wrapper for sniffles 2020-08-29 https://github.com/fritzsedlazeck/Sniffles 2.5.2 sniffles 2.5.2 Up-to-date Sequence Analysis Sequence analysis, Structural variation detection Sequence analysis, Structural variation detection DNA structural variation, Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 134 1141 1141 156 156 606 606 80 80 2267 2267 370 1110 4014 12042
+snipit snipit Summarise snps relative to a reference sequence 2022-07-17 https://github.com/aineniamh/snipit 1.6 snipit 1.6 Up-to-date Variant Analysis, Sequence Analysis Base position variability plotting Base position variability plotting Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit snipit snipit Summarise snps relative to a reference sequence 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 44 44 905 905 0 0 0 0 0 0 0 0 44 132 905 2715
+snippy snippy_core, snippy, snippy_clean_full_aln Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 3448 3602 121363 124773 3945 3945 92504 92504 2705 3073 48068 52034 10098 30816 261935 793181
+snp_dists snp_dists Compute pairwise SNP distance matrix from a FASTA sequence alignment 2019-10-18 https://github.com/tseemann/snp-dists 0.8.2 snp-dists 0.8.2 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 807 807 6555 6555 171 171 5336 5336 182 182 1143 1143 1160 3480 13034 39102
+snp_sites snp_sites Finds SNP sites from a multi-FASTA alignment file 2017-06-28 https://github.com/sanger-pathogens/snp-sites 2.5.1 snp-sites 2.5.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 663 663 6597 6597 256 256 1467 1467 114 114 1279 1279 1033 3099 9343 28029
+snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names SnpEff is a genetic variant annotation and effect prediction toolbox 2014-11-11 http://snpeff.sourceforge.net/ 5.2 biopython 1.70 To update Genome-Wide Association Study, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff 5 5 5 0 0 0 0 0 0 0 0 1 0 0 0 0 5 5 0 0 0 0 0 5 0 0 0 0 0 0 5 5 5 0 7181 7908 103826 108296 15871 22769 115727 178110 2148 2321 11817 13155 25200 83398 231370 762301
+snpeff_sars_cov_2 snpeff_sars_cov_2 SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox 2020-06-17 http://snpeff.sourceforge.net/ To update Genome-Wide Association Study, Variant Analysis SNP detection SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs DNA polymorphism, Nucleic acid sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1276 1276 764895 764895 1636 1636 94572 94572 561 561 26990 26990 3473 10419 886457 2659371
+snpfreqplot snpfreqplot A plotting app to visualise the SNPs across a region 2020-12-02 https://github.com/BrownfieldPlantLab/SNPFreqPlot 1.0 r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 338 338 3683 3683 433 433 1401 1401 95 95 1029 1029 866 2598 6113 18339
+snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck snpEff SnpSift tools from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift 8 8 8 0 0 0 0 0 0 0 0 8 0 0 0 0 0 8 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 3602 4283 5142904 5146618 7013 9678 382391 421190 960 1184 104030 105024 11575 38295 5629325 16931482
snpsift_dbnsfp snpSift_dbnsfp snpEff SnpSift dbnsfp tool from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 24 52 55 75 75 421 421 0 0 0 0 98 295 473 1422
snpsift_genesets snpSift_geneSets Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#geneSets snpsift 5.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 128 509 554 190 190 474 474 0 0 0 0 297 912 983 2994
-socru socru Order and orientation of complete bacterial genomes 2019-09-03 https://github.com/quadram-institute-bioscience/socru 2.1.7 socru 2.2.4 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 42 42 659 659 92 92 296 296 0 0 0 0 134 402 955 2865
-sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
-spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades 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. 2016-12-21 https://github.com/ablab/spades 3.15.5 spades 4.0.0 To update Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – 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. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 0 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8209 8526 82716 87113 14787 14790 120471 120475 5817 6653 54067 61541 28813 87595 257254 783637
-spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 2019-01-11 http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ 2.4.9 python To update Sequence Analysis, Genome annotation iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 91 100 450 491 288 288 4270 4270 0 0 0 0 379 1146 4720 14201
+socru socru Order and orientation of complete bacterial genomes 2019-09-03 https://github.com/quadram-institute-bioscience/socru 2.1.7 socru 2.2.4 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 42 42 659 659 92 92 296 296 0 0 0 0 134 402 955 2865
+sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/katholt/sonneityping https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
+spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades 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. 2016-12-21 https://github.com/ablab/spades 3.15.5 spades 4.0.0 To update Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – 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. 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8209 8526 82716 87113 14787 14790 120471 120475 5817 6653 54067 61541 28813 87595 257254 783637
+spaln list_spaln_tables, spaln Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 2019-01-11 http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ 2.4.9 python To update Sequence Analysis, Genome annotation iuc https://github.com/ogotoh/spaln https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 91 100 450 491 288 288 4270 4270 0 0 0 0 379 1146 4720 14201
spapros spapros_evaluation, spapros_selection Select and evaluate probe sets for targeted spatial transcriptomics. 2024-08-25 https://github.com/theislab/spapros 0.1.5 spapros 0.1.5 Up-to-date Single Cell, Transcriptomics, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spotyping spotyping SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-07 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 23 23 1436 1436 0 0 0 0 0 0 0 0 23 69 1436 4308
spyboat spyboat Wavelet analysis for 3d-image stacks 2020-11-28 http://github.com/tensionhead/spyboat 0.1.2 spyboat To update Imaging, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 5 5 142 142 0 0 0 0 0 0 0 0 5 15 142 426
-sra_tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities 2015-11-16 https://github.com/ncbi/sra-tools 3.1.1 sra-tools 3.1.1 Up-to-date Data Source, Fastq Manipulation Data handling Data handling DNA, Genomics, Sequencing DNA, Genomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 2 0 3 0 0 0 0 0 0 3 0 0 0 0 0 0 3 3 3 0 16710 17342 364871 376580 53271 59638 583675 678448 5910 6181 48131 50455 75891 234943 996677 3098837
-srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.21 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 297 297 1 1 71 71 0 0 0 0 41 123 368 1104
-stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2016-03-07 http://catchenlab.life.illinois.edu/stacks/ stacks 2.65 To update Sequence Analysis Data handling Data handling Mapping, Population genetics Mapping, Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. 0 13 13 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 465 593 6440 11998 0 0 0 0 76 76 4070 4070 541 1751 10510 37088
-star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 2015-10-15 https://github.com/STAR-Fusion/STAR-Fusion 0.5.4-3+galaxy1 star-fusion 1.14.0 To update Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 82 95 1312 1383 234 303 2198 3076 3 3 173 173 319 1039 3683 11998
+sra_tools fasterq_dump, fastq_dump, sam_dump NCBI Sequence Read Archive toolkit utilities 2015-11-16 https://github.com/ncbi/sra-tools 3.1.1 sra-tools 3.1.1 Up-to-date Data Source, Fastq Manipulation Data handling Data handling DNA, Genomics, Sequencing DNA, Genomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 2 0 3 0 0 0 0 0 3 0 0 0 0 0 0 3 3 3 0 16710 17342 364871 376580 53271 59638 583675 678448 5910 6181 48131 50455 75891 234943 996677 3098837
+srst2 srst2 SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.21 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/katholt/srst2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 40 40 297 297 1 1 71 71 0 0 0 0 41 123 368 1104
+stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2016-03-07 http://catchenlab.life.illinois.edu/stacks/ stacks 2.65 To update Sequence Analysis Data handling Data handling Mapping, Population genetics Mapping, Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. 0 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 13 0 465 593 6440 11998 0 0 0 0 76 76 4070 4070 541 1751 10510 37088
+star_fusion star_fusion STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 2015-10-15 https://github.com/STAR-Fusion/STAR-Fusion 0.5.4-3+galaxy1 star-fusion 1.14.0 To update Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 82 95 1312 1383 234 303 2198 3076 3 3 173 173 319 1039 3683 11998
straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion Toolbox to optimize biological model 2022-10-02 https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.3 To update Systems Biology, Synthetic Biology iuc https://github.com/brsynth/straindesign https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 2021-01-27 https://github.com/Illumina/strelka/ 2.9.10 strelka 2.9.10 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 112 112 669 669 417 417 1261 1261 0 0 0 0 529 1587 1930 5790
-stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 2014-09-13 http://ccb.jhu.edu/software/stringtie/ 2.2.3 stringtie 2.2.3 Up-to-date Transcriptomics Transcriptome assembly, RNA-Seq analysis Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-Seq Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 4972 5347 178677 187728 10825 15171 320780 407379 1032 1167 26375 28921 16829 55343 525832 1675692
-structure structure for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html 2.3.4 structure 2.3.4 Up-to-date Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 118 123 2858 3001 0 0 0 0 0 0 0 0 118 359 2858 8717
+strelka strelka_germline, strelka_somatic Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 2021-01-27 https://github.com/Illumina/strelka/ 2.9.10 strelka 2.9.10 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 112 112 669 669 417 417 1261 1261 0 0 0 0 529 1587 1930 5790
+stringtie stringtie, stringtie_merge StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 2014-09-13 http://ccb.jhu.edu/software/stringtie/ 2.2.3 stringtie 2.2.3 Up-to-date Transcriptomics Transcriptome assembly, RNA-Seq analysis Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-Seq Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 0 4972 5347 178677 187728 10825 15171 320780 407379 1032 1167 26375 28921 16829 55343 525832 1675692
+structure structure for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html 2.3.4 structure 2.3.4 Up-to-date Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 118 123 2858 3001 0 0 0 0 0 0 0 0 118 359 2858 8717
structureharvester structureharvester for parsing STRUCTURE outputs and for performing the Evanno method 2017-12-06 http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ 0.6.94 structureharvester 0.6.94 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
suite_pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. 2021-04-05 https://github.com/wtsi-hpag/PretextSnapshot 0.0.7 pretextgraph 0.0.7 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 3 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 538 538 3463 3463 256 256 1853 1853 70 70 1097 1097 864 2592 6413 19239
swiftlink swiftlink Parallel MCMC Linkage Analysis 2017-11-21 https://github.com/ajm/swiftlink 1.0 swiftlink 1.0 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
syndiva syndiva SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. 2022-06-23 1.0 clustalo 1.2.4 To update Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 30 30 0 0 0 0 0 0 0 0 2 6 30 90
-table_compute table_compute Perform general-purpose table operations 2019-06-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1811 1814 216072 216115 1558 1558 12326 12326 256 256 16136 16136 3625 10878 244534 733645
-tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 449 482 7011 8135 626 2183 9473 28494 80 104 850 1090 1155 5079 17334 72387
-tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2016-05-05 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup 1.0.2 openjdk To update Statistics, SAM, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 16 158 164 40 73 722 865 0 0 0 0 55 199 880 2789
+table_compute table_compute Perform general-purpose table operations 2019-06-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute 1.2.4 pandas To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1811 1814 216072 216115 1558 1558 12326 12326 256 256 16136 16136 3625 10878 244534 733645
+tabular_to_fastq tabular_to_fastq Tabular to FASTQ converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.1.5 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 449 482 7011 8135 626 2183 9473 28494 80 104 850 1090 1155 5079 17334 72387
+tag_pileup_frequency tag_pileup_frequency Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2016-05-05 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup 1.0.2 openjdk To update Statistics, SAM, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 15 16 158 164 40 73 722 865 0 0 0 0 55 199 880 2789
tasmanian_mismatch tasmanian_mismatch Analysis of positional mismatches 2020-04-19 https://github.com/nebiolabs/tasmanian-mismatch 1.0.7 tasmanian-mismatch 1.0.7 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 4 4 7 7 61 61 0 0 0 0 11 33 65 195
taxonkit name2taxid, profile2cami TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.18.0 taxonkit 0.18.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/shenwei356/taxonkit https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy 2019-01-13 https://github.com/pvanheus/ncbitaxonomy 0.3.0 rust-ncbitaxonomy 1.0.7 To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1+galaxy0 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 5257 5431 36069 36922 5066 5826 25255 30822 1584 1584 7949 7949 11907 36655 69273 214239
-taxpasta taxpasta standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ 0.7.0 taxpasta 0.7.0 Up-to-date Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 34 34 0 0 0 0 0 0 0 0 5 15 34 102
+taxonomy_filter_refseq taxonomy_filter_refseq Filter RefSeq by taxonomy 2019-01-13 https://github.com/pvanheus/ncbitaxonomy 0.3.0 rust-ncbitaxonomy 1.0.7 To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+taxonomy_krona_chart taxonomy_krona_chart Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1+galaxy0 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 5257 5431 36069 36922 5066 5826 25255 30822 1584 1584 7949 7949 11907 36655 69273 214239
+taxpasta taxpasta standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ 0.7.0 taxpasta 0.7.0 Up-to-date Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/taxprofiler/taxpasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 34 34 0 0 0 0 0 0 0 0 5 15 34 102
tb_variant_filter tb_variant_filter M. tuberculosis H37Rv VCF filter 2019-10-03 https://github.com/COMBAT-TB/tb_variant_filter 0.4.0 tb_variant_filter 0.4.0 Up-to-date Variant Analysis iuc https://github.com/COMBAT-TB/tb_variant_filter https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 461 461 22977 22977 274 274 3888 3888 80 80 3611 3611 815 2445 30476 91428
-tbl2gff3 tbl2gff3 Table to GFF3 2020-07-07 https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 466 466 1941 1941 0 0 0 0 112 112 463 463 578 1734 2404 7212
+tbl2gff3 tbl2gff3 Table to GFF3 2020-07-07 https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 466 466 1941 1941 0 0 0 0 112 112 463 463 578 1734 2404 7212
tbprofiler tb_profiler_profile Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. 2019-04-02 https://github.com/jodyphelan/TBProfiler 6.4.0 delly 1.3.1 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 372 379 6372 6395 378 378 7339 7339 154 154 6966 6966 904 2719 20677 62054
tbvcfreport tbvcfreport Generate HTML report from SnpEff M.tuberculosis VCF(s) 2019-08-29 https://github.com/COMBAT-TB/tbvcfreport 1.0.1 tbvcfreport 1.0.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 335 335 2955 2955 348 348 6090 6090 72 72 2347 2347 755 2265 11392 34176
te_finder te_finder Transposable element insertions finder 2022-08-08 https://github.com/VistaSohrab/TEfinder 1.0.1 samtools 1.21 To update Sequence Analysis Genome indexing, Variant calling, PCR primer design Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 203 203 0 0 0 0 0 0 0 0 20 60 203 609
telescope_assign telescope_assign Single locus resolution of Transposable ELEment expression. 2019-09-03 https://github.com/mlbendall/telescope/ 1.0.3 telescope 1.0.3 Up-to-date Genome annotation Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tetoolkit tetoolkit_tetranscripts The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. 2020-04-10 http://hammelllab.labsites.cshl.edu/software/ 2.2.3 tetranscripts 2.2.3 Up-to-date Sequence Analysis iuc https://github.com/mhammell-laboratory/TEtranscripts https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 74 74 1013 1013 0 0 0 0 4 4 70 70 78 234 1083 3249
-tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. 2019-11-23 https://github.com/aesheppard/TETyper 1.1 tetyper 1.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 16 106 106 47 47 155 155 0 0 0 0 63 189 261 783
+tetyper tetyper Type a specific transposable element (TE) of interest from paired-end sequencing data. 2019-11-23 https://github.com/aesheppard/TETyper 1.1 tetyper 1.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 16 16 106 106 47 47 155 155 0 0 0 0 63 189 261 783
tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter Compute distances between sequences 2018-06-06 https://github.com/veg/tn93/ 1.0.14 tn93 1.0.14 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 42 42 1915 1915 225 225 1972 1972 0 0 0 0 267 801 3887 11661
-tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files 2024-04-30 https://gitlab.com/ifb-elixirfr/abromics/tooldistillator 0.9.1 tooldistillator 0.9.1 Up-to-date Sequence Analysis Data handling, Parsing Parsing Microbiology, Bioinformatics, Sequence analysis Microbiology, Bioinformatics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator tooldistillator ToolDistillator 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. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 65 65 5 5 6 6 0 0 0 0 14 42 71 213
-transdecoder transdecoder TransDecoder finds coding regions within transcripts 2015-11-09 https://transdecoder.github.io/ 5.5.0 transdecoder 5.7.1 To update Transcriptomics, RNA Coding region prediction, de Novo sequencing, De-novo assembly Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 944 970 5964 6418 1066 1066 5450 5450 317 344 2610 2796 2327 7034 14024 42712
+tooldistillator tooldistillator, tooldistillator_summarize ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files 2024-04-30 https://gitlab.com/ifb-elixirfr/abromics/tooldistillator 0.9.1 tooldistillator 0.9.1 Up-to-date Sequence Analysis Data handling, Parsing Parsing Microbiology, Bioinformatics, Sequence analysis Microbiology, Bioinformatics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator tooldistillator ToolDistillator 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. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 65 65 5 5 6 6 0 0 0 0 14 42 71 213
+transdecoder transdecoder TransDecoder finds coding regions within transcripts 2015-11-09 https://transdecoder.github.io/ 5.5.0 transdecoder 5.7.1 To update Transcriptomics, RNA Coding region prediction, de Novo sequencing, De-novo assembly Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 944 970 5964 6418 1066 1066 5450 5450 317 344 2610 2796 2327 7034 14024 42712
transtermhp transtermhp Finds rho-independent transcription terminators in bacterial genomes 2015-10-08 https://transterm.cbcb.umd.edu transtermhp 2.09 To update Sequence Analysis Transcriptional regulatory element prediction Transcriptional regulatory element prediction Transcription factors and regulatory sites Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp TransTermHP 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 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 31 31 250 254 45 45 174 174 0 0 0 0 76 228 424 1276
-trimal trimal Tool for automated alignment trimming 2024-10-02 https://trimal.readthedocs.io 1.5.0 trimal 1.5.0 Up-to-date Sequence Analysis, Phylogenetics Multiple sequence alignment Multiple sequence alignment Sequence analysis, Sequencing, Sequence sites, features and motifs Sequence analysis, Sequencing, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal trimal trimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data 2024-01-03 http://www.usadellab.org/cms/?page=trimmomatic 0.39 trimmomatic 0.39 Up-to-date Fastq Manipulation pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 14547 15408 352353 383014 39323 49850 632385 839058 5268 5975 125340 139097 59138 189509 1110078 3581325
+trimal trimal Tool for automated alignment trimming 2024-10-02 https://trimal.readthedocs.io 1.5.0 trimal 1.5.0 Up-to-date Sequence Analysis, Phylogenetics Multiple sequence alignment Multiple sequence alignment Sequence analysis, Sequencing, Sequence sites, features and motifs Sequence analysis, Sequencing, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal trimal trimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+trimmomatic trimmomatic A flexible read trimming tool for Illumina NGS data 2024-01-03 http://www.usadellab.org/cms/?page=trimmomatic 0.39 trimmomatic 0.39 Up-to-date Fastq Manipulation pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 0 0 0 1 1 0 1 1 1 0 14547 15408 352353 383014 39323 49850 632385 839058 5268 5975 125340 139097 59138 189509 1110078 3581325
trimns trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline 2021-01-29 https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs 0.1.0 trimns_vgp 1.0 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 43 43 0 0 0 0 0 0 0 0 20 60 43 129
-trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. 2016-11-15 https://trinotate.github.io/ 3.2.2 trinotate 4.0.2 To update Transcriptomics, RNA Gene functional annotation Gene functional annotation Gene expression, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 374 390 1968 2080 527 527 1825 1825 161 195 862 1060 1062 3236 4655 14275
-trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers 2021-02-11 https://github.com/rrwick/Trycycler 0.5.5 trycycler 0.5.5 Up-to-date Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 265 265 14681 14681 0 0 0 0 147 147 4488 4488 412 1236 19169 57507
-tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 2017-05-26 https://cran.r-project.org/web/packages/Rtsne/ 0.0.2 r-rtsne 0.13 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 31 37 255 379 64 64 281 281 0 0 0 0 95 291 536 1732
-tximport tximport Wrapper for the Bioconductor package tximport 2019-10-15 http://bioconductor.org/packages/tximport/ 1.30.0 bioconductor-tximport 1.30.0 Up-to-date Transcriptomics Pathway or network analysis, Formatting, RNA-Seq analysis Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Transcriptomics, Gene transcripts, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 225 225 1802 1802 904 904 6963 6963 0 0 0 0 1129 3387 8765 26295
+trinotate trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. 2016-11-15 https://trinotate.github.io/ 3.2.2 trinotate 4.0.2 To update Transcriptomics, RNA Gene functional annotation Gene functional annotation Gene expression, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 374 390 1968 2080 527 527 1825 1825 161 195 862 1060 1062 3236 4655 14275
+trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers 2021-02-11 https://github.com/rrwick/Trycycler 0.5.5 trycycler 0.5.5 Up-to-date Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 265 265 14681 14681 0 0 0 0 147 147 4488 4488 412 1236 19169 57507
+tsne tsne T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 2017-05-26 https://cran.r-project.org/web/packages/Rtsne/ 0.0.2 r-rtsne 0.13 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 31 37 255 379 64 64 281 281 0 0 0 0 95 291 536 1732
+tximport tximport Wrapper for the Bioconductor package tximport 2019-10-15 http://bioconductor.org/packages/tximport/ 1.30.0 bioconductor-tximport 1.34.0 To update Transcriptomics Pathway or network analysis, Formatting, RNA-Seq analysis Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Transcriptomics, Gene transcripts, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 225 225 1802 1802 904 904 6963 6963 0 0 0 0 1129 3387 8765 26295
ucsc_axtchain ucsc_axtchain Chain together genome alignments 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-axtchain 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_axttomaf ucsc_axtomaf Convert dataset from axt to MAF format. 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-axttomaf 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_blat ucsc_blat Standalone blat sequence search command line tool 2017-05-17 http://genome.ucsc.edu/goldenPath/help/blatSpec.html 472 ucsc-blat 472 Up-to-date Sequence Analysis Sequence alignment Sequence alignment Sequence analysis Sequence analysis yating-l https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat blat BLAT Fast, accurate spliced alignment of DNA sequences. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainnet ucsc_chainnet Make alignment nets out of chains 2024-08-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainnet 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainprenet ucsc_chainprenet Remove chains that don't have a chance of being netted 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainprenet 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_chainsort ucsc_chainsort Sort chains. By default sorts by score. 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-chainsort 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-ucsc_fasplit fasplit faSplit is a tool to split a single FASTA file into several files 2017-09-08 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-fasplit 469 Up-to-date Fasta Manipulation Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 460 478 3278 3361 595 595 6144 6144 183 183 1139 1139 1238 3732 10561 31766
+ucsc_fasplit fasplit faSplit is a tool to split a single FASTA file into several files 2017-09-08 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-fasplit 469 Up-to-date Fasta Manipulation Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 460 478 3278 3361 595 595 6144 6144 183 183 1139 1139 1238 3732 10561 31766
ucsc_fatovcf fatovcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs 2023-01-11 http://hgdownload.cse.ucsc.edu/admin/exe/ 473 ucsc-fatovcf 473 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 385 385 107 107 587 587 5 5 58 58 158 474 1030 3090
ucsc_maftoaxt maftoaxt Convert dataset from MAF to axt format 2024-07-30 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-maftoaxt 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_netfilter ucsc_netfilter Filter out parts of net 2024-09-18 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-netfilter 469 Up-to-date Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -1077,107 +1079,107 @@ ucsc_netsyntenic ucsc_netsyntenic Add synteny info to a net dataset 2024-09-04 h
ucsc_nettoaxt ucsc_nettoaxt Convert net (and chain) to axt format. 2024-09-19 http://hgdownload.cse.ucsc.edu/admin/exe/ 469 ucsc-nettoaxt 469 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ucsc_twobittofa ucsc-twobittofa twoBitToFa is a tool to convert all or part of .2bit file to FASTA 2016-08-19 https://genome.ucsc.edu/goldenpath/help/twoBit.html 472 ucsc-twobittofa 472 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 84 118 413 511 123 123 441 441 2 2 21 21 209 661 875 2723
ucsc_wigtobigwig ucsc_wigtobigwig converts bedGraph (wig) files into binary bigwig 2024-01-14 https://genome.ucsc.edu/goldenPath/help/bigWig.html 472 ucsc-wigtobigwig 472 Up-to-date Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 106 106 1601 1601 172 172 1108 1108 15 15 200 200 293 879 2909 8727
-unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. 2017-05-08 https://github.com/rrwick/Unicycler 0.5.1 unicycler 0.5.1 Up-to-date Assembly Genome assembly, Aggregation Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Microbiology, Genomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3798 3963 74120 77648 5451 7380 64946 90075 2010 2080 19516 20422 11259 35941 158582 505309
+unicycler unicycler Unicycler is a hybrid assembly pipeline for bacterial genomes. 2017-05-08 https://github.com/rrwick/Unicycler 0.5.1 unicycler 0.5.1 Up-to-date Assembly Genome assembly, Aggregation Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Microbiology, Genomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3798 3963 74120 77648 5451 7380 64946 90075 2010 2080 19516 20422 11259 35941 158582 505309
usher usher_matutils, usher UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.2.1 usher 0.6.3 To update Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher usher usher 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. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 5 5 1060 1060 0 0 0 0 0 0 0 0 5 15 1060 3180
-valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 87 518 677 65 65 234 234 0 0 0 0 140 432 752 2415
+valet valet A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 75 87 518 677 65 65 234 234 0 0 0 0 140 432 752 2415
vapor vapor Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/connor-lab/vapor 1.0.2 vapor 1.0.2 Up-to-date Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor vapor VAPOR 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. 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 147 147 5936 5936 15 15 523 523 0 0 0 0 162 486 6459 19377
vardict_java vardict_java VarDict - calls SNVs and indels for tumour-normal pairs 2020-08-21 https://github.com/AstraZeneca-NGS/VarDictJava 1.8.3 python To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 37 37 381 381 0 0 0 0 0 0 0 0 37 111 381 1143
variant_analyzer mut2read, mut2sscs, read2mut Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data 2019-11-20 2.0.0 matplotlib To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 14 14 95 95 67 67 516 516 0 0 0 0 81 243 611 1833
-varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data 2018-07-10 https://dkoboldt.github.io/varscan/ 2.4.3 varscan 2.4.6 To update Variant Analysis iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1442 1560 10711 11502 3135 3135 16705 16705 100 100 1036 1036 4677 14149 28452 86147
+varscan varscan_copynumber, varscan_mpileup, varscan_somatic VarScan is a variant caller for high-throughput sequencing data 2018-07-10 https://dkoboldt.github.io/varscan/ 2.4.3 varscan 2.4.6 To update Variant Analysis iuc https://github.com/galaxyproject/iuc/tree/master/tools/varscan https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 1442 1560 10711 11502 3135 3135 16705 16705 100 100 1036 1036 4677 14149 28452 86147
varvamp varvamp Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.2.1 varvamp 1.2.1 Up-to-date Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/jonas-fuchs/varVAMP https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 273 273 0 0 0 0 0 0 0 0 12 36 273 819
-vcf2maf vcf2maf vcf2maf: Convert VCF into MAF 2022-06-28 https://github.com/mskcc/vcf2maf 1.6.21 vcf2maf 1.6.22 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 1097 1097 0 0 0 0 5 5 65 65 51 153 1162 3486
-vcf2tsv vcf2tsv Converts VCF files into tab-delimited format 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 823 874 169090 169679 1141 2594 16304 42215 169 172 2485 2511 2133 7906 187879 590163
-vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 32 882 888 36 114 6118 8261 6 6 175 184 72 296 7175 23683
-vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 897 1219 6879 17157 1245 1925 7585 14509 225 229 1648 1681 2367 8107 16112 65571
+vcf2maf vcf2maf vcf2maf: Convert VCF into MAF 2022-06-28 https://github.com/mskcc/vcf2maf 1.6.21 vcf2maf 1.6.22 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 1097 1097 0 0 0 0 5 5 65 65 51 153 1162 3486
+vcf2tsv vcf2tsv Converts VCF files into tab-delimited format 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 823 874 169090 169679 1141 2594 16304 42215 169 172 2485 2511 2133 7906 187879 590163
+vcfaddinfo vcfaddinfo Adds info fields from the second dataset which are not present in the first dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 30 32 882 888 36 114 6118 8261 6 6 175 184 72 296 7175 23683
+vcfallelicprimitives vcfallelicprimitives Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 897 1219 6879 17157 1245 1925 7585 14509 225 229 1648 1681 2367 8107 16112 65571
vcfanno vcfanno Annotate VCF files 2021-01-17 https://github.com/brentp/vcfanno 0.3.5 vcfanno 0.3.5 Up-to-date Variant Analysis SNP annotation SNP annotation Genetic variation, Data submission, annotation and curation Genetic variation, Data submission, annotation and curation iuc https://github.com/galaxyproject/tools-iuc/vcfanno/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 174 174 1139 1139 0 0 0 0 0 0 0 0 174 522 1139 3417
-vcfannotate vcfannotate Intersect VCF records with BED annotations 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 157 181 2797 2850 652 1392 3668 14532 61 63 494 507 870 3376 6959 31807
-vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 66 189 203 155 387 497 1828 11 11 184 197 228 920 870 3968
-vcfbedintersect vcfbedintersect Intersect VCF and BED datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 210 3017 4049 406 1147 4709 20250 40 42 507 527 631 2661 8233 41292
-vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 40 416 478 82 309 3969 10457 8 8 362 378 125 607 4747 20807
-vcfcheck vcfcheck Verify that the reference allele matches the reference genome 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 106 745 767 222 627 803 1895 16 17 241 256 334 1418 1789 6496
-vcfcombine vcfcombine Combine multiple VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 284 505 1422 2020 1021 2669 4951 19530 60 62 493 516 1365 5966 6866 35798
-vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 42 233 253 79 287 234 1839 11 12 199 214 127 595 666 3638
-vcfdistance vcfdistance Calculate distance to the nearest variant. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 92 572 585 139 296 2063 2427 19 22 272 290 248 906 2907 9116
-vcffilter vcffilter2 Tool for filtering VCF files 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2113 2218 37489 47142 5730 10533 75128 162296 320 331 2626 2736 8163 29408 115243 442660
-vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 173 926 957 313 985 2291 5323 28 31 251 265 496 2181 3468 13481
-vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 21 25 172 183 67 201 351 879 15 16 312 342 103 448 835 3074
-vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 112 778 794 179 508 2414 3721 20 21 209 225 306 1253 3401 11542
-vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 143 502 555 266 858 3428 6338 23 24 220 235 423 1871 4150 15428
-vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 182 186 1964 1991 188 644 1937 3846 26 27 567 601 396 1649 4468 15374
-vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 38 42 269 310 89 287 358 1071 12 14 179 213 139 621 806 3206
-vcfprimers vcfprimers Extract flanking sequences for each VCF record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 33 590 711 75 200 403 831 10 12 190 214 113 471 1183 4122
-vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 15 161 168 27 75 153 350 6 6 184 192 46 188 498 1706
-vcfselectsamples vcfselectsamples Select samples from a VCF file 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 69 88 830 900 237 959 1315 6257 20 21 344 363 326 1720 2489 12498
-vcfsort vcfsort Sort VCF dataset by coordinate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 185 1868 1904 422 1279 18378 24175 70 73 537 674 666 2869 20783 68319
-vcfvcfintersect vcfvcfintersect Intersect two VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 703 748 976544 977015 981 2103 64155 81830 225 229 11044 11069 1909 6898 1051743 3173400
+vcfannotate vcfannotate Intersect VCF records with BED annotations 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 157 181 2797 2850 652 1392 3668 14532 61 63 494 507 870 3376 6959 31807
+vcfannotategenotypes vcfannotategenotypes Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 62 66 189 203 155 387 497 1828 11 11 184 197 228 920 870 3968
+vcfbedintersect vcfbedintersect Intersect VCF and BED datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 185 210 3017 4049 406 1147 4709 20250 40 42 507 527 631 2661 8233 41292
+vcfbreakcreatemulti vcfbreakcreatemulti Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 35 40 416 478 82 309 3969 10457 8 8 362 378 125 607 4747 20807
+vcfcheck vcfcheck Verify that the reference allele matches the reference genome 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 96 106 745 767 222 627 803 1895 16 17 241 256 334 1418 1789 6496
+vcfcombine vcfcombine Combine multiple VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 284 505 1422 2020 1021 2669 4951 19530 60 62 493 516 1365 5966 6866 35798
+vcfcommonsamples vcfcommonsamples Output records belonging to samples commong between two datasets. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 37 42 233 253 79 287 234 1839 11 12 199 214 127 595 666 3638
+vcfdistance vcfdistance Calculate distance to the nearest variant. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 90 92 572 585 139 296 2063 2427 19 22 272 290 248 906 2907 9116
+vcffilter vcffilter2 Tool for filtering VCF files 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2113 2218 37489 47142 5730 10533 75128 162296 320 331 2626 2736 8163 29408 115243 442660
+vcffixup vcffixup Count the allele frequencies across alleles present in each record in the VCF file. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 155 173 926 957 313 985 2291 5323 28 31 251 265 496 2181 3468 13481
+vcfflatten vcfflatten2 Removes multi-allelic sites by picking the most common alternate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 21 25 172 183 67 201 351 879 15 16 312 342 103 448 835 3074
+vcfgeno2haplo vcfgeno2haplo Convert genotype-based phased alleles into haplotype alleles 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 107 112 778 794 179 508 2414 3721 20 21 209 225 306 1253 3401 11542
+vcfgenotypes vcfgenotypes Convert numerical representation of genotypes to allelic. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 143 502 555 266 858 3428 6338 23 24 220 235 423 1871 4150 15428
+vcfhethom vcfhethom Count the number of heterozygotes and alleles, compute het/hom ratio. 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 182 186 1964 1991 188 644 1937 3846 26 27 567 601 396 1649 4468 15374
+vcfleftalign vcfleftalign Left-align indels and complex variants in VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 38 42 269 310 89 287 358 1071 12 14 179 213 139 621 806 3206
+vcfprimers vcfprimers Extract flanking sequences for each VCF record 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 28 33 590 711 75 200 403 831 10 12 190 214 113 471 1183 4122
+vcfrandomsample vcfrandomsample Randomly sample sites from VCF dataset 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 13 15 161 168 27 75 153 350 6 6 184 192 46 188 498 1706
+vcfselectsamples vcfselectsamples Select samples from a VCF file 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 69 88 830 900 237 959 1315 6257 20 21 344 363 326 1720 2489 12498
+vcfsort vcfsort Sort VCF dataset by coordinate 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 174 185 1868 1904 422 1279 18378 24175 70 73 537 674 666 2869 20783 68319
+vcfvcfintersect vcfvcfintersect Intersect two VCF datasets 2017-01-24 https://github.com/ekg/vcflib vcflib 1.0.10 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 703 748 976544 977015 981 2103 64155 81830 225 229 11044 11069 1909 6898 1051743 3173400
velocyto velocyto_cli Velocyto is a library for the analysis of RNA velocity. 2021-04-30 http://velocyto.org/ 0.17.17 velocyto.py 0.17.17 Up-to-date Transcriptomics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 7 7 6 6 22 22 1 1 16 16 11 33 45 135
-velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 3899 4270 25171 27943 7557 7557 51187 51187 3585 3613 28546 28619 15041 45522 104904 317557
-velvetoptimiser velvetoptimiser Automatically optimize Velvet assemblies 2017-12-19 2.2.6+galaxy2 velvet 1.2.10 To update Assembly Optimisation and refinement, Sequence assembly Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Genomics, Sequence assembly simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser velvetoptimiser VelvetOptimiser 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 965 4715 5343 2117 2117 9575 9576 1050 1397 3271 5524 4055 12589 17561 55565
+velvet velvetg, velveth de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 3899 4270 25171 27943 7557 7557 51187 51187 3585 3613 28546 28619 15041 45522 104904 317557
+velvetoptimiser velvetoptimiser Automatically optimize Velvet assemblies 2017-12-19 2.2.6+galaxy2 velvet 1.2.10 To update Assembly Optimisation and refinement, Sequence assembly Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Genomics, Sequence assembly simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser velvetoptimiser VelvetOptimiser 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. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 888 965 4715 5343 2117 2117 9575 9576 1050 1397 3271 5524 4055 12589 17561 55565
verkko verkko Telomere-to-telomere assembly pipeline 2023-01-24 https://github.com/marbl/verkko 1.3.1 verkko 2.2.1 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 25 25 48 48 0 0 0 0 0 0 0 0 25 75 48 144
-virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers 2024-03-04 https://github.com/marieBvr/virAnnot 1.1.0+galaxy0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot virannot virAnnot "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." 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 94 94 0 0 0 0 0 0 0 0 16 48 94 282
+virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers 2024-03-04 https://github.com/marieBvr/virAnnot 1.1.0+galaxy0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot virannot virAnnot "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." 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 16 94 94 0 0 0 0 0 0 0 0 16 48 94 282
virheat virheat generates a heatmap of allele frequencies from vcf files 2024-05-15 https://github.com/jonas-fuchs/virHEAT 0.7.1 virheat 0.7.3 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 12 12 0 0 0 0 0 0 0 0 2 6 12 36
virhunter virhunter Deep Learning method for novel virus detection in sequencing data 2022-09-13 https://github.com/cbib/virhunter 1.0.0 numpy To update Machine Learning Sequence classification Sequence classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 76 76 574 574 0 0 0 0 0 0 0 0 76 228 574 1722
-volcanoplot volcanoplot Tool to create a Volcano Plot 2018-10-01 https://ggplot2.tidyverse.org/ 0.0.6 r-ggplot2 2.2.1 To update Visualization, Transcriptomics, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3670 3786 34917 36852 5597 5597 54931 54931 905 905 7183 7183 10172 30632 97031 293028
-vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.29.1 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch vsearch VSEARCH 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. 8 8 8 8 0 0 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 559 628 9694 10338 1031 2007 12282 53546 246 277 5334 5672 1836 6584 27310 124176
+volcanoplot volcanoplot Tool to create a Volcano Plot 2018-10-01 https://ggplot2.tidyverse.org/ 0.0.6 r-ggplot2 2.2.1 To update Visualization, Transcriptomics, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 3670 3786 34917 36852 5597 5597 54931 54931 905 905 7183 7183 10172 30632 97031 293028
+vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.29.1 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch vsearch VSEARCH 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. 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 0 0 0 0 8 0 0 0 0 0 0 8 8 8 0 559 628 9694 10338 1031 2007 12282 53546 246 277 5334 5672 1836 6584 27310 124176
vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. 2020-04-26 https://github.com/USDA-VS/vSNP 3.0.6 pysam 0.22.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-weblogo3 rgweblogo3 Sequence Logo generator for fasta 2017-11-17 3.5.0 weblogo 3.7.9 To update Graphics Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Nucleic acid sites, features and motifs, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 weblogo WebLogo Web-based application designed to make generate sequence logos. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 206 228 2720 2818 1354 3657 10299 30578 50 59 1226 1285 1610 7164 14245 63171
+weblogo3 rgweblogo3 Sequence Logo generator for fasta 2017-11-17 3.5.0 weblogo 3.7.9 To update Graphics Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Nucleic acid sites, features and motifs, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 weblogo WebLogo Web-based application designed to make generate sequence logos. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 206 228 2720 2818 1354 3657 10299 30578 50 59 1226 1285 1610 7164 14245 63171
windowmasker windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker 2023-12-14 https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ 1.0 blast 2.16.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 537 537 7 7 12 12 2 2 297 297 28 84 846 2538
winnowmap winnowmap A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. 2021-04-29 https://github.com/marbl/Winnowmap 2.03 winnowmap 2.03 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 46 46 279 279 4 4 12 12 0 0 0 0 50 150 291 873
xpath xpath XPath XML querying tool 2015-04-14 http://search.cpan.org/dist/XML-XPath/ perl-xml-xpath 1.47 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 7 8 128 235 0 1 0 1 0 0 0 0 7 23 128 492
yahs yahs Yet Another Hi-C scaffolding tool 2022-06-28 https://github.com/c-zhou/yahs 1.2a.2 yahs 1.2.2 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 176 176 618 618 62 62 336 336 25 25 588 588 263 789 1542 4626
zerone zerone ChIP-seq discretization and quality control 2018-09-05 https://github.com/nanakiksc/zerone 1.0 zerone 1.0 Up-to-date ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 9 12 83 96 0 0 0 0 0 0 0 0 9 30 83 262
- artic_guppyplex, artic_minion 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 2020-04-17 https://github.com/artic-network/fieldbioinformatics artic 1.5.7 To update Sequence Analysis Sequence alignment Sequence alignment Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 238 238 9021 9021 0 0 0 0 0 0 0 0 238 714 9021 27063
+ artic_guppyplex, artic_minion 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 2020-04-17 https://github.com/artic-network/fieldbioinformatics artic 1.5.8 To update Sequence Analysis Sequence alignment Sequence alignment Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 238 238 9021 9021 0 0 0 0 0 0 0 0 238 714 9021 27063
b2btools_single_sequence This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. 2022-08-09 https://bio2byte.be 3.0.5+galaxy0 b2btools 3.0.7 To update Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology Protein disorder prediction, Protein secondary structure prediction, Protein feature detection Protein disorder prediction, Protein secondary structure prediction iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 19 19 369 369 0 0 0 0 0 0 0 0 19 57 369 1107
bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ BCFtools toolkit wrappers 2015-08-12 https://samtools.github.io/bcftools/ 1.15.1 bcftools 1.21 To update Variant Analysis Data handling, Variant calling Data handling, Variant calling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment DNA polymorphism, GWAS study, Genotyping experiment iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 2017-10-05 https://github.com/dmaticzka/bctools 0.2.2 bctools 0.2.2 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 7 0 234 265 2352 3092 0 0 0 0 0 0 0 0 234 733 2352 7796
- bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 2016-11-03 https://pypi.python.org/pypi/biopython-extensions/ 0.21.9 python-bioext 0.21.9 Up-to-date Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 822 822 17413 17413 2020 2020 15349 15349 1 1 2 2 2843 8529 32764 98292
- biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.15 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format biomformat biomformat "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." 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 297 297 12725 12725 450 638 2851 5049 214 239 2171 2371 961 3096 17747 55639
+ bioext_bam2msa, bioext_bealign A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 2016-11-03 https://pypi.python.org/pypi/biopython-extensions/ 0.21.9 python-bioext 0.21.9 Up-to-date Next Gen Mappers iuc https://github.com/davebx/bioext-gx/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 822 822 17413 17413 2020 2020 15349 15349 1 1 2 2 2843 8529 32764 98292
+ biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.15 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format biomformat biomformat "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." 2 2 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 297 297 12725 12725 450 638 2851 5049 214 239 2171 2371 961 3096 17747 55639
cherri_eval, cherri_train Computational Help Evaluating RNA-RNA interactions 2022-12-09 https://github.com/BackofenLab/Cherri 0.7 cherri 0.8 To update Transcriptomics, RNA Molecular interactions, pathways and networks, Structure analysis, Machine learning Molecular interactions, pathways and networks, Structure analysis, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 1 207 207 0 0 0 0 0 0 0 0 1 3 207 621
- datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. 2015-08-03 https://www.gnu.org/software/datamash/ 1.8 datamash 1.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 3 3 3 3 0 0 0 0 0 0 0 0 0 0 1 3 3 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 7066 7307 748586 760943 5306 6131 98089 112831 2161 2171 16235 16317 14533 44675 862910 2615911
+ datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. 2015-08-03 https://www.gnu.org/software/datamash/ 1.8 datamash 1.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 1 3 3 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 7066 7307 748586 760943 5306 6131 98089 112831 2161 2171 16235 16317 14533 44675 862910 2615911
dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. 2023-07-19 https://github.com/cbib/DIMet 0.2.4 dimet 0.2.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.15 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 1408 1408 8648 8648 6 6 32 32 597 597 6406 6406 2011 6033 15086 45258
- ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin 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. 2017-05-26 https://github.com/tidyverse/ggplot2 3.4.0 r-base To update Visualization Visualisation Visualisation Data visualisation Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 3463 3630 24606 25662 5143 5144 26805 26808 1259 1279 8174 8237 9865 29783 59585 179877
+ funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.15 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). 3 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 0 1408 1408 8648 8648 6 6 32 32 597 597 6406 6406 2011 6033 15086 45258
+ ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin 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. 2017-05-26 https://github.com/tidyverse/ggplot2 3.4.0 r-base To update Visualization Visualisation Visualisation Data visualisation Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 1 0 5 0 0 0 0 0 3 0 0 0 0 0 0 5 5 5 0 3463 3630 24606 25662 5143 5144 26805 26808 1259 1279 8174 8237 9865 29783 59585 179877
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 Glimmer makes gene predictions. 2017-11-28 https://ccb.jhu.edu/software/glimmer/ glimmer 3.02 To update Sequence Analysis Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer gemini GEMINI 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. 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 407 407 4343 4343 0 0 0 0 0 0 0 0 407 1221 4343 13029
- goenrichment, goslimmer Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment 2.0.1 goenrichment 2.0.1 Up-to-date Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 826 871 5800 6212 1048 1048 7756 7756 215 215 1149 1149 2089 6312 14705 44527
+ goenrichment, goslimmer Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment 2.0.1 goenrichment 2.0.1 Up-to-date Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 826 871 5800 6212 1048 1048 7756 7756 215 215 1149 1149 2089 6312 14705 44527
gvcftools_extract_variants gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. 2016-12-29 https://github.com/sequencing/gvcftools 0.1 gvcftools 0.17.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- gwastools_manhattan_plot 2019-10-07 https://bioconductor.org/packages/release/bioc/html/GWASTools.html 0.1.0 bioconductor-gwastools 1.48.0 To update Visualization, Variant Analysis Deposition, Analysis, Annotation Deposition, Analysis, Annotation GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ gwastools_manhattan_plot 2019-10-07 https://bioconductor.org/packages/release/bioc/html/GWASTools.html 0.1.0 bioconductor-gwastools 1.48.0 To update Visualization, Variant Analysis Deposition, Analysis, Annotation Deposition, Analysis, Annotation GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hicstuff_pipeline A toolkit to generate and manipulate Hi-C matrices 2022-11-25 https://github.com/koszullab/hicstuff 3.2.4 hicstuff 3.2.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer 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). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis 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 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 Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 hmmer3 HMMER3 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. 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 1283 1321 35919 36952 0 0 0 0 180 180 3023 3023 1463 4427 38942 117859
- 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 Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.47 hyphy 2.5.64 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 17 2 17 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 428 428 11429 11429 676 676 7751 7751 58 58 715 715 1162 3486 19895 59685
- kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. 2017-08-04 https://pachterlab.github.io/kallisto/ 0.48.0 kallisto 0.51.1 To update Transcriptomics Gene expression profiling Gene expression profiling Transcriptomics, RNA-Seq, Gene expression Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 932 965 28398 29031 2603 3025 73705 80087 218 230 5333 5567 3753 11726 107436 329557
- lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. 2019-11-25 https://csb5.github.io/lofreq/ 2.1.5 lofreq 2.1.5 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 5 5 5 4 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4301 4301 4176367 4176367 8213 8213 509615 509615 1815 1815 106342 106342 14329 42987 4792324 14376972
- mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 2017-11-08 https://sourceforge.net/projects/mageck/ 0.5.9.2 mageck 0.5.9.5 To update Genome editing Genetic variation analysis Genetic variation analysis Genetics, Genetic variation, Genomics Genetics, Genetic variation, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 3 5 5 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 873 889 11761 12093 473 473 5762 5762 343 343 5610 5610 1689 5083 23133 69731
- maker, maker_map_ids 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. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.03 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1315 1366 6417 6861 1858 1858 7235 7235 902 902 4112 4112 4075 12276 17764 53736
- mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash 2018-12-07 https://github.com/marbl/Mash 2.3 mash 2.3 Up-to-date Metagenomics Sequence distance matrix generation Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash mash Mash Fast genome and metagenome distance estimation using MinHash. 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 61 61 10119 10119 9 9 19 19 7 7 647 647 77 231 10785 32355
- medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 1.7.2 medaka 2.0.1 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka medaka Medaka 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. 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 1693 1693 117975 117975 796 796 55063 55063 639 639 9325 9325 3128 9384 182363 547089
+ hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer 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). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis 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 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 Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 hmmer3 HMMER3 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. 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 12 0 1283 1321 35919 36952 0 0 0 0 180 180 3023 3023 1463 4427 38942 117859
+ 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 Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.47 hyphy 2.5.64 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 17 2 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 12 17 12 0 428 428 11429 11429 676 676 7751 7751 58 58 715 715 1162 3486 19895 59685
+ kallisto_pseudo, kallisto_quant kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. 2017-08-04 https://pachterlab.github.io/kallisto/ 0.48.0 kallisto 0.51.1 To update Transcriptomics Gene expression profiling Gene expression profiling Transcriptomics, RNA-Seq, Gene expression Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 932 965 28398 29031 2603 3025 73705 80087 218 230 5333 5567 3753 11726 107436 329557
+ lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. 2019-11-25 https://csb5.github.io/lofreq/ 2.1.5 lofreq 2.1.5 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 4 0 0 0 0 0 0 5 5 5 0 4301 4301 4176367 4176367 8213 8213 509615 509615 1815 1815 106342 106342 14329 42987 4792324 14376972
+ mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 2017-11-08 https://sourceforge.net/projects/mageck/ 0.5.9.2 mageck 0.5.9.5 To update Genome editing Genetic variation analysis Genetic variation analysis Genetics, Genetic variation, Genomics Genetics, Genetic variation, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 3 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 873 889 11761 12093 473 473 5762 5762 343 343 5610 5610 1689 5083 23133 69731
+ maker, maker_map_ids 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. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.03 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1315 1366 6417 6861 1858 1858 7235 7235 902 902 4112 4112 4075 12276 17764 53736
+ mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash 2018-12-07 https://github.com/marbl/Mash 2.3 mash 2.3 Up-to-date Metagenomics Sequence distance matrix generation Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash mash Mash Fast genome and metagenome distance estimation using MinHash. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 61 61 10119 10119 9 9 19 19 7 7 647 647 77 231 10785 32355
+ medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 1.7.2 medaka 2.0.1 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka medaka Medaka 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. 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 2 0 0 0 0 0 0 3 3 3 0 1693 1693 117975 117975 796 796 55063 55063 639 639 9325 9325 3128 9384 182363 547089
metaeuk_easy_predict 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. 2020-08-04 https://github.com/soedinglab/metaeuk 7.bba0d80 metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 40 40 312 312 0 0 0 0 0 0 0 0 40 120 312 936
- miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.13 miniprot 0.13 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot miniprot miniprot 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. 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 86 86 1244 1244 15 15 24 24 0 0 0 0 101 303 1268 3804
+ miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.13 miniprot 0.13 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot miniprot miniprot 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. 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 86 86 1244 1244 15 15 24 24 0 0 0 0 101 303 1268 3804
bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) 2022-04-11 https://github.com/BlankenbergLab/nAltORFs 0.1.2 naltorfs 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 75 204 204 0 0 0 0 75 225 204 612
- nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain 2021-03-29 https://github.com/nextstrain/nextclade 2.7.0 nextalign 2.14.0 To update Sequence Analysis Methylation analysis, Variant calling Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics Genomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 396 396 4411 4411 279 279 9708 9708 212 212 2099 2099 887 2661 16218 48654
- ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. 2015-11-10 https://github.com/ngsutils/ngsutils ngsutils 0.5.9 To update SAM Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 633 716 24611 29662 740 1128 15523 21395 125 145 7751 8972 1498 4985 47885 155799
- odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 2020-04-06 https://github.com/vgteam/odgi 0.3 odgi 0.9.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6 6 26 26 0 0 0 0 0 0 0 0 6 18 26 78
+ nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain 2021-03-29 https://github.com/nextstrain/nextclade 2.7.0 nextalign 2.14.0 To update Sequence Analysis Methylation analysis, Variant calling Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics Genomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 396 396 4411 4411 279 279 9708 9708 212 212 2099 2099 887 2661 16218 48654
+ ngsutils_bam_filter NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. 2015-11-10 https://github.com/ngsutils/ngsutils ngsutils 0.5.9 To update SAM Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 633 716 24611 29662 740 1128 15523 21395 125 145 7751 8972 1498 4985 47885 155799
+ odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 2020-04-06 https://github.com/vgteam/odgi 0.3 odgi 0.9.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 6 6 26 26 0 0 0 0 0 0 0 0 6 18 26 78
pizzly Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. 2017-09-03 https://github.com/pmelsted/pizzly/ 0.37.3.1 pizzly 0.37.3 To update Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 23 24 201 210 76 76 998 998 0 0 0 0 99 298 1199 3606
- poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 2017-12-17 https://poretools.readthedocs.io/en/latest/ 0.6.1a1 poretools 0.6.1a1 Up-to-date Fasta Manipulation, Fastq Manipulation Nucleic acid sequence analysis Nucleic acid sequence analysis DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 13 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 1055 1245 19942 20587 2183 2594 33619 40808 365 365 9261 9261 3603 11410 62822 196300
- qq_manhattan 2020-10-07 https://CRAN.R-project.org/package=qqman 0.1.0 r-qqman 0.1.4 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 2017-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3 3 3 1 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 1265 1305 130124 135361 922 922 11135 11135 153 153 5939 5939 2340 7060 147198 446831
- raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis 2018-03-03 https://github.com/dgrun/RaceID3_StemID2_package/ 0.2.3 r-raceid 0.1.3 To update Single Cell, Transcriptomics Expression profile clustering, Expression analysis, Molecular dynamics Expression profile clustering, Expression analysis, Molecular dynamics Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid RaceID RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data 5 5 5 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 395 518 3077 4581 1093 1093 2856 2856 19 19 1977 1977 1507 4644 7910 25234
- raven Raven is a de novo genome assembler for long uncorrected reads. 2020-11-04 https://github.com/lbcb-sci/raven 1.8.3 raven-assembler 1.8.3 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 438 438 9477 9477 0 0 0 0 182 182 10585 10585 620 1860 20062 60186
- cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast 2017-05-26 https://cran.r-project.org/web/packages/reshape2/index.html 1.4.2 r-reshape2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 2 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 108 111 3543 3619 157 157 536 536 0 0 0 0 265 798 4079 12313
+ poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 2017-12-17 https://poretools.readthedocs.io/en/latest/ 0.6.1a1 poretools 0.6.1a1 Up-to-date Fasta Manipulation, Fastq Manipulation Nucleic acid sequence analysis Nucleic acid sequence analysis DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 13 13 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 0 1055 1245 19942 20587 2183 2594 33619 40808 365 365 9261 9261 3603 11410 62822 196300
+ qq_manhattan 2020-10-07 https://CRAN.R-project.org/package=qqman 0.1.0 r-qqman 0.1.4 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ filter_tabular, query_tabular, sqlite_to_tabular Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 2017-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 1 0 0 0 0 0 0 3 3 3 0 1265 1305 130124 135361 922 922 11135 11135 153 153 5939 5939 2340 7060 147198 446831
+ raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory RaceID3, StemID2, FateID - scRNA analysis 2018-03-03 https://github.com/dgrun/RaceID3_StemID2_package/ 0.2.3 r-raceid 0.1.3 To update Single Cell, Transcriptomics Expression profile clustering, Expression analysis, Molecular dynamics Expression profile clustering, Expression analysis, Molecular dynamics Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid RaceID RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 395 518 3077 4581 1093 1093 2856 2856 19 19 1977 1977 1507 4644 7910 25234
+ raven Raven is a de novo genome assembler for long uncorrected reads. 2020-11-04 https://github.com/lbcb-sci/raven 1.8.3 raven-assembler 1.8.3 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 438 438 9477 9477 0 0 0 0 182 182 10585 10585 620 1860 20062 60186
+ cast, melt Flexibly restructure and aggregate data using just the two functions melt and dcast 2017-05-26 https://cran.r-project.org/web/packages/reshape2/index.html 1.4.2 r-reshape2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 108 111 3543 3619 157 157 536 536 0 0 0 0 265 798 4079 12313
ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data 2022-09-22 https://github.com/LabTranslationalArchitectomics/riboWaltz 1.2.0 ribowaltz 2.0 To update Transcriptomics, RNA Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 20 20 171 171 0 0 0 0 0 0 0 0 20 60 171 513
scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. 2019-07-18 http://bioconductor.org/packages/scater/ 1.22.0 bioconductor-scater 1.30.1 To update Single Cell, Transcriptomics, Visualization Read pre-processing, Sequencing quality control, Sequence visualisation Read pre-processing, Sequence visualisation RNA-Seq, Quality affairs, Molecular genetics RNA-Seq, Quality affairs, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 5 0 350 351 1345 1371 0 0 0 0 29 29 903 903 379 1138 2248 6770
seqcomplexity Sequence complexity for raw reads 2022-06-07 https://github.com/stevenweaver/seqcomplexity 0.1.2 seqcomplexity 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 19 19 70 70 47 47 109 109 0 0 0 0 66 198 179 537
seqwish Alignment to variation graph inducer 2020-04-06 https://github.com/ekg/seqwish 0.7.5 seqwish 0.7.11 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 2 2 271 271 0 0 0 0 0 0 0 0 2 6 271 813
sinto_barcode, sinto_fragments Sinto single-cell analysis tools 2023-04-12 https://github.com/timoast/sinto 0.10.1 sinto 0.10.1 Up-to-date Single Cell, Epigenetics Bioinformatics, Cell biology Bioinformatics, Cell biology iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto sinto sinto Sinto is a toolkit for processing aligned single-cell data. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 70 70 284 284 38 38 165 165 2 2 14 14 110 330 463 1389
- stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2018-12-01 http://catchenlab.life.illinois.edu/stacks/ 2.55 stacks 2.65 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 0 12 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 626 646 8437 8592 0 0 0 0 270 270 18016 18016 896 2708 26453 79514
- tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 2024-03-28 https://github.com/cbib/TraceGroomer 0.1.4 tracegroomer 0.1.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 0 0 0 0 1 3 7 21
+ stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2018-12-01 http://catchenlab.life.illinois.edu/stacks/ 2.55 stacks 2.65 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 0 12 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 12 0 626 646 8437 8592 0 0 0 0 270 270 18016 18016 896 2708 26453 79514
+ tracegroomer TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 2024-03-28 https://github.com/cbib/TraceGroomer 0.1.4 tracegroomer 0.1.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 0 0 0 0 0 0 0 0 1 3 7 21
tracy_align, tracy_assemble, tracy_basecall, tracy_decompose 2021-10-12 0.6.1 tracy 0.7.8 To update iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 124 124 3314 3314 0 0 0 0 0 0 0 0 124 372 3314 9942
gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps TRANSIT 2019-03-01 https://github.com/mad-lab/transit/ 3.0.2 transit 3.2.3 To update Genome annotation Transposon prediction Transposon prediction DNA, Sequencing, Mobile genetic elements DNA, Sequencing, Mobile genetic elements iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit transit TRANSIT 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. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 5 5 0 189 189 1039 1039 467 485 2672 3349 47 47 358 358 703 2127 4069 12884
- trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq 2015-11-09 https://github.com/trinityrnaseq/trinityrnaseq 2.15.1 trinity 2.15.2 To update Transcriptomics, RNA Transcriptome assembly Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Transcriptomics, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. 9 13 13 13 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 4376 4632 35698 39132 6714 6714 44509 44509 1924 2070 21883 23889 13014 39444 102090 311710
- tsebra This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 17 17 0 0 0 0 0 0 0 0 7 21 17 51
- umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq 2017-08-09 https://github.com/CGATOxford/UMI-tools 1.1.5 umi_tools 1.1.5 Up-to-date Sequence Analysis, Transcriptomics, Single Cell Sequencing quality control Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Sequence sites, features and motifs, Quality affairs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. 5 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 1090 1223 55050 68123 906 906 9001 9001 187 187 12444 12444 2183 6682 76495 242558
- vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 198 209 2157 2287 446 744 3930 5591 0 0 0 0 644 2241 6087 20052
- vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 2020-04-08 https://github.com/vgteam/vg 1.23.0 vg 1.61.0 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 17 17 478 478 0 0 0 0 0 0 0 0 17 51 478 1434
- bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 401 401 9073 9073 224 224 2746 2746 10 10 103 103 635 1905 11922 35766
+ trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq 2015-11-09 https://github.com/trinityrnaseq/trinityrnaseq 2.15.1 trinity 2.15.2 To update Transcriptomics, RNA Transcriptome assembly Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Transcriptomics, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. 9 13 13 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 11 0 0 1 0 0 0 11 13 12 0 4376 4632 35698 39132 6714 6714 44509 44509 1924 2070 21883 23889 13014 39444 102090 311710
+ tsebra This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 17 17 0 0 0 0 0 0 0 0 7 21 17 51
+ umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq 2017-08-09 https://github.com/CGATOxford/UMI-tools 1.1.5 umi_tools 1.1.6 To update Sequence Analysis, Transcriptomics, Single Cell Sequencing quality control Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Sequence sites, features and motifs, Quality affairs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 5 0 0 0 0 0 0 3 5 5 0 1090 1223 55050 68123 906 906 9001 9001 187 187 12444 12444 2183 6682 76495 242558
+ vegan_diversity, vegan_fisher_alpha, vegan_rarefaction an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 198 209 2157 2287 446 744 3930 5591 0 0 0 0 644 2241 6087 20052
+ vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 2020-04-08 https://github.com/vgteam/vg 1.23.0 vg 1.61.0 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 3 0 17 17 478 478 0 0 0 0 0 0 0 0 17 51 478 1434
+ bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett. 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.2 bamtools 2.5.2 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 401 401 9073 9073 224 224 2746 2746 10 10 103 103 635 1905 11922 35766
2017-01-24 https://github.com/samtools/samtools 1.20 samtools 1.21 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Geometric means (Dead wood) Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). 2023-11-10 https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom 0.1.0+galaxy0 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 18 53 53 0 0 0 0 0 0 0 0 18 54 53 159
MALDIquant maldi_quant_peak_detection, maldi_quant_preprocessing MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. 2018-08-22 http://strimmerlab.org/software/maldiquant/ 1.22.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 61 68 1452 3822 0 0 0 0 39 39 1065 1065 100 307 2517 9921
@@ -1186,7 +1188,7 @@ Make data paper sketches from EML data_paper_from_EML This tool derived from the
QCxMS qcxms_getres, qcxms_neutral_run, qcxms_production_run QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD). 2023-08-24 https://github.com/grimme-lab/QCxMS 5.2.1 To update Computational chemistry, Molecular Dynamics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 11246 11246 0 0 0 0 0 0 0 0 13 39 11246 33738
SCCAF run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out SCCAF: Single Cell Clustering Assessment Framework. 2019-10-20 https://github.com/sccaf/sccaf 0.0.9 sccaf 0.0.10 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf 4 3 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 110 110 0 0 0 0 0 0 0 0 19 57 110 330
ab1fastq ab1_fastq_converter Tool to convert ab1 files into FASTQ files 2021-10-08 1.20.0 bioconductor-sangerseqr 1.38.0 To update Convert Formats ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 281 281 49465 49465 0 0 0 0 0 0 0 0 281 843 49465 148395
-ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. 2019-06-13 http://ambermd.org/AmberTools.php 21.10 ambertools To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 7 2 7 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 510 511 41793 41881 159 159 1126 1126 85 85 1552 1552 754 2263 44471 133501
+ambertools ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories. 2019-06-13 http://ambermd.org/AmberTools.php 21.10 ambertools To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools 7 2 7 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 7 5 0 510 511 41793 41881 159 159 1126 1126 85 85 1552 1552 754 2263 44471 133501
appendfdr append_fdr 2015-01-24 0.2.0 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
artbio_bam_cleaning artbio_bam_cleaning filter bam files before somatic-varscan or lumpy-smoove analysis 2020-10-02 http://artbio.fr 1.10+galaxy0 samtools 1.21 To update SAM, Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
astronomicalarchivestool astronomical_archives Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy 2023-07-17 0.10.0 astropy To update Data Source astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/ https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 6 6 53 53 0 0 0 0 0 0 0 0 6 18 53 159
@@ -1195,34 +1197,34 @@ atlas_fastq_provider fastq_provider Retrieval and download of FASTQ files from E
bamparse bamparse Generates hit count lists from bam alignments. 2017-10-12 http://artbio.fr 4.1.1 pysam 0.22.1 To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
baseline_toxicity_calculator tt_baseline Toxicity prediction using QSAR models 2024-03-25 https://github.com/bernt-matthias/mb-galaxy-tools 0.1.0+galaxy0 pandas To update Ecology, Text Manipulation mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
bed_to_protein_map bed_to_protein_map Converts a BED file to a tabular list of exon locations 2018-01-04 0.2.0 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 134 137 410 419 99 99 363 363 13 13 158 158 246 741 931 2802
-bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format 2021-10-06 http://artbio.fr 377+galaxy1 ucsc-bigwigtobedgraph 469 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 567 650 5769 6802 0 0 0 0 0 1 0 3 567 1785 5769 18343
+bigwig_to_bedgraph bigwig_to_bedgraph Converts a bigWig file to bedGraph format 2021-10-06 http://artbio.fr 377+galaxy1 ucsc-bigwigtobedgraph 469 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 567 650 5769 6802 0 0 0 0 0 1 0 3 567 1785 5769 18343
bigwig_to_wig bigwig_to_wig Converts a bigWig file to Wiggle (WIG) format 2018-09-25 https://artbio.fr 3+galaxy0 ucsc-bigwiginfo 469 To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. 2018-10-03 http://thegrantlab.org/bio3d/index.php 2.4_1 r-bio3d 2.3_3 To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 5 4 5 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 1150 1159 10600 10729 255 255 1042 1042 215 215 2756 2756 1620 4869 14398 43323
+bio3d bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize Bio3d is a program that can be used to analyse molecular dynamics trajectories. 2018-10-03 http://thegrantlab.org/bio3d/index.php 2.4_1 r-bio3d 2.3_3 To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d 5 4 5 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 5 0 1150 1159 10600 10729 255 255 1042 1042 215 215 2756 2756 1620 4869 14398 43323
biobb_pytorch biobb_pytorch_apply_mdae, biobb_pytorch_train_mdae biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular [PyTorch](https://pytorch.org/) Python library. 2024-06-26 https://github.com/bioexcel/biobb_pytorch 4.2.1 biobb_pytorch 5.0.0 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biobb_pytorch 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
biomoldyn biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering Tools for MD analysis 2020-01-30 https://github.com/moldyn/ 1.5.2 scipy To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 119 119 493 493 148 148 441 441 0 0 0 0 267 801 934 2802
biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. 2020-08-26 https://bitbucket.org/djoumbou/biotransformerjar/src/master/ 3.0.20230403 biotransformer 3.0.20230403 Up-to-date Metabolomics Metabolic pathway prediction, PTM site prediction, Natural product identification Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 48 48 1 3 48 144
blast2go blast2go Maps BLAST results to GO annotation terms 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go 0.0.11 b2g4pipe To update Ontology Manipulation, Sequence Analysis Gene functional annotation Gene functional annotation Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go Blast2GO Blast2GO Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 257 300 1063 1237 0 0 0 0 0 0 0 0 257 814 1063 3363
-blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option 2015-01-24 https://blast.ncbi.nlm.nih.gov/ 2.6.0 blast 2.16.0 To update Sequence Analysis galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 283 347 24916 27120 0 0 0 0 0 0 0 0 283 913 24916 76952
-blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs 2016-01-05 http://artbio.fr 1.1.0 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 1 3 8 24
-blast_unmatched blast_unmatched Extract unmatched query sequences from blast 2017-10-03 http://artbio.fr 1.0.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits 2017-10-15 http://artbio.fr 2.7.1 python To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 1 3 8 24
-blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs 2015-06-17 http://artbio.fr 1.1.1 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 483 552 264392 265217 0 0 0 0 0 0 0 0 483 1518 264392 794001
+blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option 2015-01-24 https://blast.ncbi.nlm.nih.gov/ 2.6.0 blast 2.16.0 To update Sequence Analysis galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+blast_rbh blast_reciprocal_best_hits BLAST Reciprocal Best Hits (RBH) from two FASTA files 2014-05-15 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh 0.3.0 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Gene functional annotation, Nucleic acid sequence analysis Gene functional annotation, Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid sites, features and motifs peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh blast_rbh blast_rbh This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 283 347 24916 27120 0 0 0 0 0 0 0 0 283 913 24916 76952
+blast_to_scaffold blast2scaffold Generate DNA scaffold from blastn or tblastx alignments of Contigs 2016-01-05 http://artbio.fr 1.1.0 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 1 3 8 24
+blast_unmatched blast_unmatched Extract unmatched query sequences from blast 2017-10-03 http://artbio.fr 1.0.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+blastparser_and_hits BlastParser_and_hits Parse blast outputs and compile hits 2017-10-15 http://artbio.fr 2.7.1 python To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 8 8 0 0 0 0 1 3 8 24
+blastx_to_scaffold blastx2scaffold Generate DNA scaffold from blastx alignment of Contigs 2015-06-17 http://artbio.fr 1.1.1 python To update RNA, Sequence Analysis, Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+blastxml_to_top_descr blastxml_to_top_descr Make table of top BLAST match descriptions 2013-09-23 https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python To update Convert Formats, Sequence Analysis, Text Manipulation Sequence alignment, Sequence annotation Sequence alignment, Sequence annotation Sequence analysis Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr blastxml_to_top_descr blastxml_to_top_descr This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 483 552 264392 265217 0 0 0 0 0 0 0 0 483 1518 264392 794001
c3s c3s Copernicus Climate Change Service (C3S) 2021-04-13 https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset 0.3.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 11 11 234 234 4 4 4 4 3 3 92 92 18 54 330 990
cads cads Copernicus Atmosphere Data Store (ADS) 2021-06-19 https://ads.atmosphere.copernicus.eu/#!/home 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 52 52 0 0 0 0 0 0 0 0 1 3 52 156
calisp calisp Calgary approach to isotopes in proteomics 2023-06-01 https://github.com/kinestetika/Calisp/ 3.0.13 calisp 3.0.13 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 2 2 0 0 0 0 0 0 0 0 2 6 2 6
-cap3 cap3 cap3 wrapper 2017-09-02 http://artbio.fr 2.0.1 cap3 10.2011 To update Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 158 158 9869 9869 0 0 0 0 146 146 6886 6886 304 912 16755 50265
+cap3 cap3 cap3 wrapper 2017-09-02 http://artbio.fr 2.0.1 cap3 10.2011 To update Assembly artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 158 158 9869 9869 0 0 0 0 146 146 6886 6886 304 912 16755 50265
cds_essential_variability cds_essential_variability Get Copernicus Essential Climate Variables for assessing climate variability 2019-05-03 https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview 0.2.0 python To update Climate Analysis, Data Source climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 39 40 232 336 0 0 0 0 0 0 0 0 39 118 232 800
cesm cesm Community Earth System Model (CESM) 2021-06-15 https://www.cesm.ucar.edu/ 2.1.3 cesm 2.1.3 Up-to-date Climate Analysis climate https://github.com/ESCOMP/CESM https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 2 14 14 0 0 0 0 0 0 0 0 2 6 14 42
checkv checkv_end_to_end Assess quality of single-contig viral genomes 2024-09-13 https://bitbucket.org/berkeleylab/checkv/ 1.0.3 checkv 1.0.3 Up-to-date Metagenomics Sequence assembly, Validation, Read mapping Sequence assembly, Validation, Read mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv checkv CheckV CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content 2015-06-17 http://artbio.fr 4.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+cherry_pick_fasta cherry_pick_fasta Pick fasta sequence with specific header content 2015-06-17 http://artbio.fr 4.1 python To update Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
climate_stripes climate_stripes Create climate stripes from a tabular input file 2019-10-05 https://www.climate-lab-book.ac.uk/2018/warming-stripes/ 1.0.2 python To update Climate Analysis, Visualization climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 35 35 239 239 2 2 16 16 3 3 182 182 40 120 437 1311
-concatenate_multiple_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. 2018-03-11 http://artbio.fr 1.4.3 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 613 614 4822 4824 204 204 1317 1317 252 289 3088 3795 1069 3245 9227 28390
-consalign aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences 2023-04-11 1.0.0 r-bioseq To update Sequence Analysis ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 154 154 1184 1184 0 0 0 0 0 0 0 0 154 462 1184 3552
+concatenate_multiple_datasets cat_multi_datasets Concatenate multiple datasets tail-to-head, including collection datasets. 2018-03-11 http://artbio.fr 1.4.3 To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 613 614 4822 4824 204 204 1317 1317 252 289 3088 3795 1069 3245 9227 28390
+consalign aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences 2023-04-11 1.0.0 r-bioseq To update Sequence Analysis ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 154 154 1184 1184 0 0 0 0 0 0 0 0 154 462 1184 3552
consolidate_vcfs consolidate_vcfs Combines freebayes and mpileup files for use by vcf2snvalignment 2015-11-05 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cooler cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify cooler different tools to process Hi-C from mirnylab 2017-07-27 https://github.com/open2c/cooler 0.9.3 htslib 1.21 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler 4 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 26 26 170 170 39 39 195 195 0 0 0 0 65 195 365 1095
-cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts 2018-07-11 http://artbio.fr 0.6.0 r-optparse 1.3.2 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+cpm_tpm_rpk cpm_tpm_rpk Generate CPM,TPM or RPK from raw counts 2018-07-11 http://artbio.fr 0.6.0 r-optparse 1.3.2 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
cta_astro_tool cta_astro_tool Basic simulation of CTA telescope observations using gammapy package 2024-04-19 0.0.1+galaxy0 unzip To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ctsm_fates ctsm_fates EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model 2020-10-21 https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api 2.0 fates-emerald To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 69 69 264 264 11 11 34 34 1 1 103 103 81 243 401 1203
custom_pro_db custom_pro_db CustomProDB 2017-10-06 https://bioconductor.org/packages/release/bioc/html/customProDB.html 1.22.0 bioconductor-rgalaxy 1.37.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 144 146 1729 1744 72 72 450 450 12 12 361 361 228 686 2540 7635
@@ -1248,34 +1250,34 @@ emlassemblyline annotations_template, eal_table_template, eal_templates, eml2eal
encyclopedia encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis 2020-09-11 https://bitbucket.org/searleb/encyclopedia/wiki/Home 1.12.34 encyclopedia 2.12.30 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia 2 4 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 98 98 738 738 1 1 1 1 4 4 42 42 103 309 781 2343
eodie eodie Earth Observation Data Information Extractor 2021-12-30 https://eodie.readthedocs.io/ 1.0.2 eodie To update Climate Analysis climate https://gitlab.com/eetun-tiimi/EODIE https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 4 45 45 0 0 0 0 0 0 0 0 4 12 45 135
ez_histograms ez_histograms ggplot2 histograms and density plots 2024-02-07 https://github.com/tidyverse/ggplot2 3.4.4 r-ggplot2 2.2.1 To update Visualization, Statistics Data analysis, Statistical calculation, Visualisation Statistical calculation, Visualisation Ecology Ecology artbio https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms ez_histograms ez_histograms This tool produces histograms or density plots from any tabular datasets, using ggplot2.You may provide headerless tables as well as tables with column headers. Any non-numeric columns will be filtered out. Your first column may contains row names, but it will also work if your first column already corresponds to the numeric values of a variable. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/ 1.2.0 python To update Fasta Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1142 1257 30917 32191 1346 1346 36869 36869 230 230 5236 5236 2718 8269 73022 220340
+fasta_merge_files_and_filter_unique_sequences fasta_merge_files_and_filter_unique_sequences Concatenate FASTA database files together 2015-01-24 https://github.com/galaxyproteomics/tools-galaxyp/ 1.2.0 python To update Fasta Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 1142 1257 30917 32191 1346 1346 36869 36869 230 230 5236 5236 2718 8269 73022 220340
fastg2protlib fastg2protlib-peptides, fastg2protlib-validate Generate FASTA from FASTG 2020-07-23 https://github.com/galaxyproteomics/fastg2protlib.git 1.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 8 8 29 29 0 0 0 0 0 0 0 0 8 24 29 87
fastq_pair fastq_pair Paired-end fastq pairer 2022-03-17 https://github.com/linsalrob/fastq-pair 1.0+galaxy0 fastq-pair 1.0 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_quality_trimmer cshl_fastq_quality_trimmer FASTQ trimmer based on quality 2022-03-11 https://github.com/agordon/fastx_toolkit 0.0.14+galaxy0 fastx_toolkit 0.0.14 To update Fastq Manipulation ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fastq_utils fastq_filter_n, fastq_trim_poly_at Set of tools for handling fastq files 2022-02-15 https://github.com/nunofonseca/fastq_utils 0.25.1+galaxy0 fastq_utils 0.25.2 To update Transcriptomics, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
feature_alignment feature_alignment TRIC integrates information from all available runs via a graph-based alignment strategy 2015-02-06 0.11.0 msproteomicstools 0.11.0 Up-to-date Proteomics galaxyp https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 18 18 0 0 0 0 0 0 0 0 1 3 18 54
-fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers 2015-06-17 http://artbio.fr 3.1.0 urllib3 1.12 To update Fasta Manipulation, Data Source artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 3 1 3
+fetch_fasta_from_ncbi retrieve_fasta_from_NCBI Fetch fasta sequences from NCBI using eutils wrappers 2015-06-17 http://artbio.fr 3.1.0 urllib3 1.12 To update Fasta Manipulation, Data Source artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 1 3 1 3
filter_by_fasta_ids filter_by_fasta_ids Filter FASTA on the headers and/or the sequences 2015-01-24 2.3 python To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 1026 1072 26717 29932 1176 1176 42990 42990 230 230 9619 9619 2432 7342 79326 241193
filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. 2021-01-06 https://github.com/RECETOX/galaxytools/ 3.1.1 openbabel 2.3.90dev7d621d9 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_density filterdensity Filter out position based on distance between SNVs 2015-11-19 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_stats filterstat SNVPhyl filter_stats 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
filter_vcf filtervcf SNVPhyl filter_vcf 2015-08-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
find_repeats findrepeat Find repetitive regions on a reference genome using MUMMer 2015-07-31 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-fishertest fishertest Fisher's exact test on two-column hit lists. 2015-06-17 http://artbio.fr 2.32.0+galaxy0 bioconductor-qvalue 2.34.0 To update RNA, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+fishertest fishertest Fisher's exact test on two-column hit lists. 2015-06-17 http://artbio.fr 2.32.0+galaxy0 bioconductor-qvalue 2.38.0 To update RNA, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
flashlfq flashlfq FlashLFQ mass-spectrometry proteomics label-free quantification 2017-12-06 https://github.com/smith-chem-wisc/FlashLFQ 1.0.3.1 flashlfq 1.2.6 To update Proteomics Label-free quantification Label-free quantification Proteomics experiment, Proteomics Proteomics experiment, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq flashlfq FlashLFQ FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 52 54 661 715 0 0 0 0 15 15 167 167 67 203 828 2538
fragpipe fragpipe Data analysis for mass spectrometry-based proteomics. 2022-07-21 https://fragpipe.nesvilab.org/ 20.0 fragpipe 20.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 64 64 0 0 0 0 0 0 0 0 9 27 64 192
freeenergy Free energy tools of BRIDGE. 2019-10-24 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-frogs 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 Suite for metabarcoding analysis 2021-08-16 http://frogs.toulouse.inrae.fr/ 4.1.0 frogs 5.0.0 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+frogs 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 Suite for metabarcoding analysis 2021-08-16 http://frogs.toulouse.inrae.fr/ 4.1.0 frogs 5.0.0 To update Metagenomics Taxonomic classification Taxonomic classification Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs frogs FROGS The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies. 0 0 0 28 0 0 0 0 0 0 0 0 0 0 0 0 18 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
from_hicup_to_juicebox fromHicupToJuicebox Convert the output of hicup (as sam or bam) to the input of juicebox. 2018-06-05 0.0.2 pysam 0.22.1 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
fromgtftobed12 fromgtfTobed12 Convert GTF files to BED12 format 2019-07-31 https://pythonhosted.org/gffutils/contents.html 0.11.1+galaxy1 gffutils 0.13 To update Convert Formats lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gatk4 filtermutectcalls, mergemutectstats, mutect2 Find somatic variations 2021-12-29 http://artbio.fr 4.1.7.0 gatk4 4.6.1.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gc_derivatization gc_derivatization In silico derivatization for GC. 2024-03-15 https://github.com/RECETOX/gc-meox-tms 1.0.1 gc-meox-tms 1.0.1 Up-to-date Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. 2019-02-25 https://www.gdal.org 3.0.0 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 0 0 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 0 39 42 1409 1498 0 0 0 0 0 0 0 0 39 120 1409 4316
genomad genomad_end_to_end Identify virus and plasmid genomes from nucleotide sequences 2024-06-17 https://github.com/apcamargo/genomad/ 1.8.0 genomad 1.8.1 To update Metagenomics Sequence annotation, Taxonomic classification Sequence annotation, Taxonomic classification Sequence analysis Sequence analysis ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad genomad geNomad geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-get_reference_fasta get_fasta_reference Obtain reference genome sequence. 2015-06-17 http://artbio.fr 0.3.2 To update Data Source, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+get_reference_fasta get_fasta_reference Obtain reference genome sequence. 2015-06-17 http://artbio.fr 0.3.2 To update Data Source, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gettn5extendedcoverage getTn5ExtendedCoverage Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension 2018-06-13 0.0.2 pysam 0.22.1 To update Epigenetics lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gffcompare_to_bed gffcompare_to_bed Filter and convert a gffCompare GTF to BED 2018-01-10 https://github.com/gpertea/gffcompare/ 0.2.1 python To update Convert Formats galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 329 347 1375 2230 362 362 1071 1071 64 64 492 492 755 2283 2938 9669
-gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. 2018-10-03 https://github.com/gromacs 2022 gromacs 2021.3 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 14 8 15 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 3441 3451 184067 184203 1438 1438 9382 9382 648 648 10325 10325 5527 16591 203774 611458
+gromacs gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids. 2018-10-03 https://github.com/gromacs 2022 gromacs 2021.3 To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs 14 8 15 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 15 9 0 3441 3451 184067 184203 1438 1438 9382 9382 648 648 10325 10325 5527 16591 203774 611458
gsc_center_scale center_scale Center or scale (standardize) data 2019-07-09 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Statistics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_cells filter_cells Filter single cell RNAseq data on library depth and number of detected genes 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gsc_filter_genes filter_genes Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data 2019-06-23 http://artbio.fr 4.3.1+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -1285,10 +1287,10 @@ gsc_mannwhitney_de mannwhitney_de Perform a mann-whitney differential testing be
gsc_scran_normalize scran_normalize Normalize raw counts using scran 2019-09-23 http://artbio.fr 1.28.1+galaxy1 bioconductor-scran 1.30.0 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 24 24 89 89 2 2 3 3 2 2 10 10 28 84 102 306
gsc_signature_score signature_score Compute signature scores from single cell RNAseq data 2019-06-23 http://artbio.fr 2.3.9+galaxy1 r-optparse 1.3.2 To update Transcriptomics, Single Cell RNA-Seq analysis, Clustering, Visualisation, Expression analysis RNA-Seq analysis, Clustering, Visualisation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score galaxy_single_cell_suite Galaxy Single Cell suite Suite of Galaxy tools from artbio.fr for end-to-end single-cell RNA-seq analysis 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
gtf2gene_list _ensembl_gtf2gene_list Utility to extract annotations from Ensembl GTF files. 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 1.52.0+galaxy0 atlas-gene-annotation-manipulation 1.1.1 To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 323 324 1982 1983 343 343 1040 1040 38 38 205 205 704 2113 3227 9682
-guppy_basecaller guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7+galaxy0 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 1 3 7 21
+guppy_basecaller guppy-basecaller A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies 2020-11-18 http://artbio.fr 6.5.7+galaxy0 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 7 7 1 3 7 21
hardklor hardklor, kronik Hardklör 2016-04-26 2.30.1+galaxy1 hardklor 2.3.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 5 8 98 111 0 0 0 0 0 0 0 0 5 18 98 307
hess_astro_tool hess_astro_tool Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope 2024-02-19 0.0.2+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
-high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps 2019-07-20 https://github.com/cran/gplots 3.1.3+galaxy0 r-gplots 2.17.0 To update Visualization artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+high_dim_heatmap high_dim_heatmap gplot heatmap.2 function adapted for plotting large heatmaps 2019-07-20 https://github.com/cran/gplots 3.1.3+galaxy0 r-gplots 2.17.0 To update Visualization artbio https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hirieftools calc_delta_pi, pi_db_split, pi_dbspec_align HiRIEF tools 2017-04-11 1.3 python To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
hyperstack_to_bleach_corrected_movie hyperstack_to_bleach_corrected_movie Generate blach corrected movie from hyperstack 2023-02-27 20230328 Fiji 20240614 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
idconvert idconvert Convert mass spectrometry identification files on linux or MacOSX 2019-02-22 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 24 33 241 276 0 0 0 0 0 0 0 0 24 81 241 758
@@ -1296,42 +1298,43 @@ incucyte_stack_and_upload_omero incucyte_stack_and_upload_omero Combine images t
iphop iphop_predict Integrated Phage Host Prediction 2024-10-14 https://bitbucket.org/srouxjgi/iphop/ 1.3.3 iphop 1.3.3 Up-to-date Metagenomics Sample comparison Sample comparison ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/iphop/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/iphop iphop iPHoP An automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
isolib isolib Create an isotopic pattern library for given compounds and adducts. 2023-10-26 https://github.com/RECETOX/galaxytools/ 2.6+galaxy0 bioconductor-metabocoreutils 1.10.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
justdiff justdiff Unix diff 2017-09-27 http://artbio.fr 3.10+galaxy0 diffutils To update Text Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-justgzip justgzip Compress fastq sequence files 2018-05-16 http://artbio.fr 2.8+galaxy0 pigz To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+justgzip justgzip Compress fastq sequence files 2018-05-16 http://artbio.fr 2.8+galaxy0 pigz To update Convert Formats artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lfq_protein_quant lfq_protein_quant Enable protein summarisation and quantitation 2018-10-02 https://github.com/compomics/LFQ_galaxy_p 1.0 bioconductor-msnbase 2.28.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 19 78 116 0 0 0 0 0 0 0 0 12 43 78 272
longorf longORF obtain longest ORF in six-frame translations 2018-06-01 0.3.0 To update Sequence Analysis mbernt https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ltq_iquant_cli 2015-01-24 To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
lumpy_smoove lumpy_smoove, vcf2hrdetect Galaxy wrapper of the lumpy-using smoove workflow 2020-07-12 http://artbio.fr 0.2.8+galaxy1 svtyper 0.7.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-lumpy_sv lumpy Find structural variations 2017-07-24 http://artbio.fr 1.3 lumpy-sv 0.3.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+lumpy_sv lumpy Find structural variations 2017-07-24 http://artbio.fr 1.3 lumpy-sv 0.3.1 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
make_nr make_nr Make a FASTA file non-redundant 2018-11-06 https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.3 biopython 1.70 To update Fasta Manipulation, Sequence Analysis Sequence alignment, Genome annotation Sequence alignment, Genome annotation Molecular biology, Sequence analysis Molecular biology, Sequence analysis peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr make_nr make_nr Make a FASTA file non-redundant, with a Galaxy wrapperThis tool is copyright 2018 by Peter Cock, The James Hutton Institute, UK. All rights reserved.This tool is a short Python script intended to be run prior to calling the NCBI BLAST+ command line tool makeblastdb or in other settings where you want to collapse duplicated sequences in a FASTA file to a single representative. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
manta manta Structural variant and indel caller for mapped sequencing data 2019-10-25 http://artbio.fr 1.6 manta 1.6.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/manta https://github.com/ARTbio/tools-artbio/tree/main/tools/manta 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 34 34 218 218 0 0 0 0 0 0 0 0 34 102 218 654
map_peptides_to_bed map_peptides_to_bed Map peptides to a reference genome for display by a genome browser 2016-01-13 0.2 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 6 7 38 44 0 0 0 0 0 0 0 0 6 19 38 120
mapping_quality_stats mapqstatistics Collects and shows the distribution of MAPQ values in a BAM alignment file 2022-06-15 http://artbio.fr 0.22.0 r-optparse 1.3.2 To update Sequence Analysis, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
matchms matchms_add_key, matchms_convert, matchms_matchms_export_skyline_transition_list, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. 2020-11-16 https://github.com/matchms/matchms 0.27.0 matchms 0.28.2 To update Metabolomics Spectral library search, Format validation, Filtering Spectral library search, Format validation, Filtering Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. 2 14 14 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 70 70 1620 1620 8 8 27 27 12 12 1685 1685 90 270 3332 9996
-maxquant maxquant, maxquant_mqpar wrapper for MaxQuant 2015-01-24 https://www.maxquant.org/ 2.0.3.0 maxquant 2.0.3.0 Up-to-date Proteomics Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1251 1264 6863 7021 543 543 2798 2798 352 352 3189 3189 2146 6451 12850 38708
-md_converter md_slicer A tool for slicing trajectory files using MDTraj. 2019-10-07 1.9.9 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 19 174 174 4 4 6 6 7 7 441 441 30 90 621 1863
+max_projections_stack_and_upload_omero max_projections_stack_and_upload_omero Combine images from max projections to stack and upload to the omero server 2024-12-12 20241213.2 Fiji 20240614 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/max_projections_stack_and_upload_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+maxquant maxquant, maxquant_mqpar wrapper for MaxQuant 2015-01-24 https://www.maxquant.org/ 2.0.3.0 maxquant 2.0.3.0 Up-to-date Proteomics Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering Proteomics experiment, Proteomics, Statistics and probability Proteomics experiment, Proteomics, Statistics and probability galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant maxquant MaxQuant Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 1251 1264 6863 7021 543 543 2798 2798 352 352 3189 3189 2146 6451 12850 38708
md_converter md_converter A tool for interconverting between different MD structure and trajectory file formats. 2018-10-13 1.9.7 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 251 253 26720 26762 54 54 784 784 53 53 977 977 358 1076 28481 85485
-mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations 2018-10-04 https://github.com/MDAnalysis/mdanalysis 1.0.0 mdanalysis To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 10 5 10 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 318 326 3209 3268 51 51 182 182 39 39 397 397 408 1232 3788 11423
+md_converter md_slicer A tool for slicing trajectory files using MDTraj. 2019-10-07 1.9.9 mdtraj To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 19 19 174 174 4 4 6 6 7 7 441 441 30 90 621 1863
+mdanalysis mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations 2018-10-04 https://github.com/MDAnalysis/mdanalysis 1.0.0 mdanalysis To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis 10 5 10 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 10 0 318 326 3209 3268 51 51 182 182 39 39 397 397 408 1232 3788 11423
mdtraj traj_selections_and_merge MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories 2020-06-24 https://github.com/mdtraj/mdtraj 1.9.7 mdtraj To update Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 8 8 36 36 4 4 63 63 0 0 0 0 12 36 99 297
mean_per_zone mean_per_zone Creates a png image showing statistic over areas as defined in the vector file 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/ 0.2.0 python To update Visualization, GIS, Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 3 3 20 25 0 0 0 0 0 0 0 0 3 9 20 65
measure_gastruloids measureGastruloids Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index 2022-01-18 20221216 fiji 20240614 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer 2017-03-03 https://github.com/compomics/meta-proteome-analyzer/ 2.0.0 mpa-portable 2.0.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 126 126 0 0 0 0 0 0 0 0 20 60 126 378
-metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ 1.0 metagene_annotator 1.0 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 323 323 980 980 0 0 0 0 0 0 0 0 323 969 980 2940
+meta_proteome_analyzer meta_proteome_analyzer MetaProteomeAnalyzer 2017-03-03 https://github.com/compomics/meta-proteome-analyzer/ 2.0.0 mpa-portable 2.0.0 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 20 20 126 126 0 0 0 0 0 0 0 0 20 60 126 378
+metagene_annotator metagene_annotator MetaGeneAnnotator gene-finding program for prokaryote and phage 2018-03-21 http://metagene.nig.ac.jp/ 1.0 metagene_annotator 1.0 Up-to-date Sequence Analysis Sequence annotation Sequence annotation Genomics, Model organisms, Data submission, annotation and curation Genomics, Model organisms, Data submission, annotation and curation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator metageneannotator MetaGeneAnnotator Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 323 323 980 980 0 0 0 0 0 0 0 0 323 969 980 2940
metanovo metanovo Produce targeted databases for mass spectrometry analysis. 2022-03-29 https://github.com/uct-cbio/proteomics-pipelines 1.9.4 metanovo 1.9.4 Up-to-date Proteomics Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo metanovo MetaNovo An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 29 29 4471 4471 0 0 0 0 0 0 0 0 29 87 4471 13413
metaquantome metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz quantitative analysis of microbiome taxonomy and function 2018-11-27 https://github.com/galaxyproteomics/metaquantome/ 2.0.2 metaquantome 2.0.2 Up-to-date Proteomics Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome metaQuantome metaQuantome 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. 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 6 0 260 262 2730 2831 0 0 0 0 71 71 1540 1540 331 995 4270 12911
mgf_formatter mgf_formatter 2014-09-26 1.0.0 mgf-formatter 1.0.0 Up-to-date galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mircounts mircounts Generates miRNA count lists from read alignments to mirBase. 2017-06-12 http://artbio.fr 1.6 tar To update RNA, Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 36 36 1458 1458 36 108 1458 4374
morpheus morpheus Morpheus MS Search Application 2015-10-29 https://cwenger.github.io/Morpheus 288 morpheus 290 To update Proteomics Peptide database search Peptide database search Proteomics Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus morpheus Morpheus A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 12 19 105 153 0 0 0 0 93 93 833 833 105 322 938 2862
-mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA 2022-03-31 https://github.com/galaxyproteomics/tools-galaxyp/ 0.1.19 bioconductor-preprocesscore 1.64.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3 3 13 13 0 0 0 0 0 0 0 0 3 9 13 39
+mqppep mqppep_anova, mqppep_preproc MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA 2022-03-31 https://github.com/galaxyproteomics/tools-galaxyp/ 0.1.19 bioconductor-preprocesscore 1.68.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3 3 13 13 0 0 0 0 0 0 0 0 3 9 13 39
ms2deepscore ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training Mass spectra similarity scoring using a trained ms2deepscore model. 2024-08-15 https://github.com/matchms/ms2deepscore 2.0.0 ms2deepscore 2.4.0 To update Metabolomics Spectrum calculation, Spectral library search, Network analysis Spectrum calculation, Spectral library search, Network analysis Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening recetox https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore ms2deepscore MS2DeepScore MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra. 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
msconvert msconvert msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container 2015-01-24 http://proteowizard.sourceforge.net/tools.shtml 3.0.20287 To update Proteomics Filtering, Formatting Filtering, Formatting Proteomics, Proteomics experiment Proteomics, Proteomics experiment galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert msconvert msConvert 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. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 455 469 20749 22184 71 71 1239 1239 53 53 2666 2666 579 1751 24654 75397
msgfplus msgfplus MSGF+ 2015-11-10 0.5 msgf_plus 2024.03.26 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 33 43 473 529 0 0 0 0 0 0 0 0 33 109 473 1475
-msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. 2019-10-23 1.0.0 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 11 110 110 0 0 0 0 0 0 0 0 11 33 110 330
+msms_extractor msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report. 2019-10-23 1.0.0 proteowizard 3_0_9992 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 11 11 110 110 0 0 0 0 0 0 0 0 11 33 110 330
msstatstmt msstatstmt MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 2021-01-20 http://msstats.org/msstatstmt/ 2.0.0 bioconductor-msstatstmt 2.10.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 104 104 795 795 0 0 0 0 12 12 461 461 116 348 1256 3768
mt2mq mt2mq Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome 2020-06-23 1.1.0 r-tidyverse To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 38 38 275 275 0 0 0 0 0 0 0 0 38 114 275 825
mutational_patterns mutational_patterns Mutational patterns and signatures in base substitution catalogs 2020-09-13 http://artbio.fr 3.12.0 bioconductor-mutationalpatterns 3.12.0 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mz_to_sqlite mz_to_sqlite Creates a SQLite database for proteomics data 2015-06-01 https://github.com/galaxyproteomics/mzToSQLite 2.1.1+galaxy0 mztosqlite 2.1.1 To update Proteomics Conversion, Peptide database search Conversion, Peptide database search Proteomics, Biological databases Proteomics, Biological databases galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite mztosqlite mzToSQLite Convert proteomics data files into a SQLite databaseExtract data from proteomics mzIdentML and mass spec scan files: mzML, MGF, etc and store in a SQLite database.The intended purpose is to provide a Galaxy dataset that can support an interactive Galaxy visualization plugin. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 110 111 854 860 15 15 79 79 13 13 274 274 138 415 1207 3627
-ncbi_blast_plus 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 NCBI BLAST+ 2013-09-23 https://blast.ncbi.nlm.nih.gov/ 2.14.1 python To update Sequence Analysis devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 16 16 16 16 0 0 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 9760 10546 391141 443752 11767 13684 306361 350178 3192 3617 227235 244814 24719 77285 924737 2888218
-oases oasesoptimiserv Short read assembler 2017-10-15 http://artbio.fr 1.4.0 oases 0.2.09 To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ncbi_blast_plus 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 NCBI BLAST+ 2013-09-23 https://blast.ncbi.nlm.nih.gov/ 2.14.1 python To update Sequence Analysis devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 16 16 16 16 0 0 0 0 0 0 0 0 0 0 0 16 15 16 0 0 0 0 0 16 0 0 0 0 16 15 16 16 15 0 9760 10546 391141 443752 11767 13684 306361 350178 3192 3617 227235 244814 24719 77285 924737 2888218
+oases oasesoptimiserv Short read assembler 2017-10-15 http://artbio.fr 1.4.0 oases 0.2.09 To update Assembly, RNA artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/oases https://github.com/ARTbio/tools-artbio/tree/main/tools/oases 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_clean_rois_tables omero_clean_rois_tables Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down 2023-06-23 20230623 fiji 20240614 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_children_ids omero_get_children_ids Get omero id of children of an omero object id 2023-12-22 0.2.0 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
omero_get_full_images omero_get_full_images Get full images from omero 2024-05-21 20240521 fiji 20240614 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -1342,7 +1345,7 @@ openmm pdbfixer OpenMM is a toolkit for molecular simulation using high performa
openms AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter OpenMS Suite for LC/MS data management and analyses 2017-02-21 https://www.openms.de/ 3.1 openms 3.2.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms 8 34 144 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 141 124 0 3316 4889 32169 108654 15 15 50 50 245 245 940 940 3576 12301 33159 175962
packmol packmol PACKMOL is a package for creating starting structures for Molecular Dynamics simulations 2018-10-04 http://m3g.iqm.unicamp.br/packmol/home.shtml 18.169.1 packmol To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 32 33 282 295 8 8 420 420 0 0 0 0 40 121 702 2119
pampa pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics 2020-06-06 0.0.2 To update Ecology ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0 5 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 4 0 146 146 1038 1038 0 0 0 0 38 38 849 849 184 552 1887 5661
-pathifier pathifier pathifier 2019-09-03 https:// 1.40.0 bioconductor-pathifier 1.40.0 Up-to-date Transcriptomics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 245 245 0 0 0 0 0 0 0 0 10 30 245 735
+pathifier pathifier pathifier 2019-09-03 https:// 1.40.0 bioconductor-pathifier 1.44.0 To update Transcriptomics, Statistics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 10 10 245 245 0 0 0 0 0 0 0 0 10 30 245 735
pep_pointer pep_pointer PepPointer categorizes peptides by their genomic coordinates. 2017-12-19 0.1.3+galaxy1 python To update Genomic Interval Operations, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 54 55 506 511 12 12 21 21 8 8 163 163 74 223 690 2075
pepquery pepquery A peptide-centric MS search engine for novel peptide identification and validation. 2020-01-22 https://pepquery.org 1.6.2 pepquery 2.0.2 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 76 76 7047 7047 0 0 0 0 0 0 0 0 76 228 7047 21141
pepquery2 pepquery2, pepquery2_index, pepquery2_show_sets PepQuery2 peptide-centric MS search for peptide identification and validation 2022-10-02 https://pepquery.org 2.0.2 pepquery 2.0.2 Up-to-date Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 3 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 28 28 1222 1222 0 0 0 0 0 0 0 0 28 84 1222 3666
@@ -1351,7 +1354,7 @@ peptideshaker fasta_cli, ident_params, peptide_shaker, search_gui PeptideShaker
pepxml_to_xls Convert PepXML to Tabular 2015-01-24 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
percolator batched_set_list_creator, percolator, percolator_input_converters, pout2mzid Percolator 2016-04-12 3.5 percolator 3.7.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator 0 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 15 16 338 378 0 0 0 0 13 13 1059 1059 28 85 1397 4231
phabox phabox_cherry, phabox_contamination, phabox_end_to_end, phabox_phagcn, phabox_phamer, phabox_phatyp, phabox_phavip, phabox_tree, phabox_votu Identify and analyze phage contigs in metagenomic data 2024-11-12 https://github.com/KennthShang/PhaBOX 2.1.5 phabox 2.1.9 To update Metagenomics Sequence assembly, Taxonomic classification, Visualisation Sequence assembly, Taxonomic classification, Visualisation Metagenomics, Microbial ecology, Sequence assembly, Taxonomy Metagenomics, Microbial ecology, Sequence assembly, Taxonomy ufz https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/phabox phabox PhaBOX Web server for identifying and characterizing phage contigs in metagenomic data. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-pindel pindel Pindel detects genome-wide structural variation. 2021-09-29 http://artbio.fr 0.2.5b9 pindel 0.2.5b9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+pindel pindel Pindel detects genome-wide structural variation. 2021-09-29 http://artbio.fr 0.2.5b9 pindel 0.2.5b9 Up-to-date Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
pmd_fdr pmd_fdr Calculate Precursor Mass Discrepancy (PMD) for MS/MS 2019-10-01 https://github.com/slhubler/PMD-FDR-for-Galaxy-P 1.4.0 r-base To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_alignment positions2snv_alignment Generate alignment of SNVs from SNVPhyl variant table. 2016-11-04 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
positions2snv_invariant_alignment positions2snv_invariant_alignment Generate alignment of SNVs and non-variant positions from SNVPhyl variant table. 2016-11-07 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Variant Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -1382,7 +1385,7 @@ rawtools rawtools Raw Tools 2019-02-28 https://github.com/kevinkovalchik/RawTool
rcx_tk rcx-tk Tools to process metadata or alkane files. 2024-08-01 https://github.com/RECETOX/rcx-tk 0.1.0+galaxy0 rcx-tk 0.1.0 To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/ https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
reactome_pathwaymatcher reactome_pathwaymatcher Reactome Pathway Matcher 2018-06-08 https://github.com/LuisFranciscoHS/PathwayMatcher pathwaymatcher 1.9.1 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 65 76 174 244 0 0 0 0 0 0 0 0 65 206 174 592
recetox-aplcms recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise Peak detection tool for HRMS profile data. 2021-06-17 https://github.com/RECETOX/recetox-aplcms 0.13.4 r-recetox-aplcms 0.13.4 Up-to-date Metabolomics Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment Metabolomics Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms recetox-aplcms recetox-aplcms recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening. 0 8 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 12 12 862 862 0 0 0 0 1 1 48 48 13 39 910 2730
-regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text 2017-01-13 1.0.3 python To update Text Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 1144 1156 78648 78834 870 870 18063 18063 194 289 4455 6051 2208 6731 101166 305280
+regex_find_replace regex1, regexColumn1 Use python regular expressions to find and replace text 2017-01-13 1.0.3 python To update Text Manipulation galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 2 0 0 0 0 0 0 2 2 2 0 1144 1156 78648 78834 870 870 18063 18063 194 289 4455 6051 2208 6731 101166 305280
rem_complex rem_complex Removes molecular coordination complexes. 2023-11-21 https://github.com/RECETOX/galaxytools 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 18 18 0 0 0 0 0 0 0 0 2 6 18 54
rename_annotated_feature rename_annotated_feature Update column names in an abundance table using a annotation table with spectral matching results 2024-05-13 https://github.com/RECETOX/galaxytools/ 1.0.0 pandas To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
repenrich edger-repenrich, repenrich Repeat element profiling 2017-05-22 https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 2.31.1 To update Transcriptomics artbio https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 57 1725 1790 56 169 1725 5240
@@ -1394,28 +1397,28 @@ rmassbank rmassbank RMassBank is an R package for processing tandem MS files and
rsem extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie transcript quantification from RNA-Seq data 2017-12-18 https://github.com/deweylab/RSEM rsem 1.3.3 To update Transcriptomics, RNA artbio https://github.com/artbio/tools-artbio/tree/master/tools/rsem https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1 1 0 158 183 363 430 0 0 0 0 13 39 67 146 171 564 430 1436
salmon_kallisto_mtx_to_10x _salmon_kallisto_mtx_to_10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 2019-11-07 https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary 0.0.1+galaxy6 scipy To update Sequence Analysis ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 172 172 682 682 74 74 322 322 3 3 3 3 249 747 1007 3021
sambamba sambamba_sample_or_filter filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM 2020-05-19 http://artbio.fr 0.7.1+galaxy1 sambamba 1.0.1 To update SAM artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 684 684 17 51 684 2052
-sashimi_plot sashimi_plot Generates a sashimi plot from bam files. 2019-08-21 http://artbio.fr 0.1.1 python To update RNA, Transcriptomics, Graphics, Visualization artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+sashimi_plot sashimi_plot Generates a sashimi plot from bam files. 2019-08-21 http://artbio.fr 0.1.1 python To update RNA, Transcriptomics, Graphics, Visualization artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scaffold scaffold, scaffold_export 2015-01-24 0.1.0 scaffold To update galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
scanpy_scripts anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data scanpy-scripts, command-line wrapper scripts around Scanpy. 2018-11-05 https://scanpy.readthedocs.io 1.9.3 scanpy-scripts 1.9.301 To update Transcriptomics, Sequence Analysis, RNA ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy 27 27 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 0 4832 4868 45501 45666 1846 1846 7304 7304 457 457 3106 3106 7135 21441 55911 167898
sceasy sceasy_convert Convert scRNA data object between popular formats 2019-10-14 0.0.5 r-sceasy 0.0.7 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 222 222 1059 1059 71 71 426 426 1 1 1 1 294 882 1486 4458
scripting tools singularity_scriptrunner suite_scripting 2023-07-29 https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ 0.1 To update Text Manipulation mbernt https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. 2024-03-29 https://cran.r-project.org/web/packages/sdmpredictors/index.html 0.2.15 r-base To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
-sequence_format_converter sequence_format_converter various fasta to tabular conversions 2017-09-04 http://artbio.fr 2.2.0 python To update Convert Formats, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+sequence_format_converter sequence_format_converter various fasta to tabular conversions 2017-09-04 http://artbio.fr 2.2.0 python To update Convert Formats, Fasta Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
sgwb_astro_tool sgwb_astro_tool SGWB 2024-04-17 0.0.1+galaxy0 ipython To update Astronomy astroteam https://github.com/esg-epfl-apc/tools-astro/tree/main/tools https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 5 5 0 0 0 0 0 0 0 0 2 6 5 15
shift_longitudes shyft_longitudes Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees 2019-03-15 https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/ 0.1.0 python To update Climate Analysis climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 4 4 54 64 0 0 0 0 0 0 0 0 4 12 54 172
-sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS 2016-10-11 0.2.4 sixgill 0.2.4 Up-to-date Proteomics, MetaProteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 71 71 312 312 0 0 0 0 0 0 0 0 71 213 312 936
+sixgill sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge Six-frame Genome-Inferred Libraries for LC-MS/MS 2016-10-11 0.2.4 sixgill 0.2.4 Up-to-date Proteomics, MetaProteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 0 71 71 312 312 0 0 0 0 0 0 0 0 71 213 312 936
small_rna_clusters small_rna_clusters clusters small rna reads in alignment BAM files 2019-10-06 http://artbio.fr 1.3.0 pysam 0.22.1 To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-small_rna_maps small_rna_maps Generates small read maps from alignment BAM files 2017-07-23 http://artbio.fr 3.1.1 numpy To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. 2017-08-28 http://artbio.fr 3.4.2 pysam 0.22.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+small_rna_maps small_rna_maps Generates small read maps from alignment BAM files 2017-07-23 http://artbio.fr 3.1.1 numpy To update RNA, SAM, Graphics, Next Gen Mappers artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+small_rna_signatures overlapping_reads, signature Computes the tendency of small RNAs to overlap with each other. 2017-08-28 http://artbio.fr 3.4.2 pysam 0.22.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
smithsonian_volcanoes smithsonian_volcanoes Retrieve data from Volcanoes of the World (VOTW) Database 2019-04-15 https://volcano.si.edu/gvp_votw.cfm 0.1.0 python To update Retrieve Data climate https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
snv_matrix snvmatrix Generate matrix of SNV distances 2016-01-21 https://snvphyl.readthedocs.io/en/latest/ 1.8.2 snvphyl-tools 1.8.2 Up-to-date Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza 2021-03-07 http://artbio.fr 3.0.0+galaxy1 sequenza-utils 3.0.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+snvtocnv sequenzaindex, snvtocnv infer copy number variations from a vcf file with SNVs using R sequenza 2021-03-07 http://artbio.fr 3.0.0+galaxy1 sequenza-utils 3.0.0 To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spec2vec spec2vec_similarity, spec2vec_training Mass spectra similarity scoring using a trained Spec2Vec model. 2022-11-29 https://github.com/iomega/spec2vec 0.8.0 spec2vec 0.8.0 Up-to-date Metabolomics Spectrum calculation, Spectral library search, Database search, Natural product identification Spectrum calculation, Spectral library search, Database search, Natural product identification Proteomics experiment, Metabolomics, Natural language processing, Proteomics Proteomics experiment, Metabolomics, Natural language processing, Proteomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec spec2vec Spec2Vec Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set. 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 3 1 3
spectrast2spectrast_irt gp_spectrast2spectrast_irt Filter from spectraST files to swath input files 2015-04-13 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spectrast2tsv gp_spectrast2tsv Filter from spectraST files to swath input files 2015-02-06 0.1.0 msproteomicstools 0.11.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
spocc_occ spocc_occ Get species occurences data 2019-05-23 https://cran.r-project.org/web/packages/spocc/index.html 1.2.2 To update Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 130 134 789 840 0 0 0 0 0 0 0 0 130 394 789 2418
-sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie sr_bowtie sr_bowtie "Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic ""Map with Bowtie for Illumina"" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis." 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 80 80 0 0 0 0 1 3 80 240
-sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. 2017-09-11 http://artbio.fr 2.8 bowtie 1.3.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+sr_bowtie bowtieForSmallRNA bowtie wrapper tool to align small RNA sequencing reads 2017-09-02 http://artbio.fr 2.3.1 bowtie 1.3.1 To update RNA, Next Gen Mappers Microbiology, Biology Microbiology artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie sr_bowtie sr_bowtie "Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25... _Bowtie: http://bowtie-bio.sourceforge.net/index.shtmlA generic ""Map with Bowtie for Illumina"" Galaxy tool is available in the main Galaxy distribution.However, this Bowtie wrapper tool only takes FASTQ files as inputs.The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis." 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 80 80 0 0 0 0 1 3 80 240
+sr_bowtie_dataset_annotation sr_bowtie_dataset_annotation Maps iteratively small RNA sequencing datasets to reference sequences. 2017-09-11 http://artbio.fr 2.8 bowtie 1.3.1 To update RNA artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
stoceps stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. 2019-09-26 0.0.2 To update Ecology ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0 0 5 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 38 38 328 328 0 0 0 0 0 0 0 0 38 114 328 984
suite_cell_types_analysis ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis 2020-04-07 1.1.1 cell-types-analysis 0.1.11 To update Transcriptomics, RNA, Statistics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 8 8 0 0 0 0 0 0 0 0 4 12 8 24
suite_decoupler score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk decoupler - Ensemble of methods to infer biological activities 2023-09-24 https://decoupler-py.readthedocs.io/en/latest/ 1.4.0+galaxy3 decoupler 1.5.0 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 54 54 0 0 0 0 0 0 0 0 6 18 54 162
@@ -1433,12 +1436,12 @@ suite_seurat seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_
suite_snvphyl_1_2_3 SNVPhyl suite defining all dependencies for SNVPhyl 2015-08-05 To update Sequence Analysis nml https://github.com/phac-nml/snvphyl-galaxy https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
tarfast5 tarfast5 produces a tar.gz archive of fast5 sequence files 2021-05-05 http://artbio.fr 0.6.1 pigz To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
thermo_raw_file_converter thermo_raw_file_converter Thermo RAW file converter 2018-09-14 https://github.com/compomics/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.5 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 88 124 2467 2959 0 0 0 0 18 18 1097 1097 106 354 3564 11184
-topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. 2021-12-23 https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 2 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 10 10 57 57 8 8 20 20 0 0 0 0 18 54 77 231
+topologyeditors gromacs_modify_topology, gromacs_extract_topology Set of python scripts and associated tool files that can be used to modify topology files. 2021-12-23 https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 0 python To update Molecular Dynamics, Computational chemistry chemteam https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 10 10 57 57 8 8 20 20 0 0 0 0 18 54 77 231
translate_bed translate_bed Translate BED transcript CDS or cDNA in 3 frames 2018-01-14 http://rest.ensembl.org/ 0.1.0 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 138 142 649 685 105 105 473 473 18 18 761 761 261 787 1883 5685
translate_bed_sequences translate_bed_sequences Perform 3 frame translation of BED file augmented with a sequence column 2016-01-13 0.2.0 biopython 1.70 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 16 21 57 69 0 0 0 0 0 0 0 0 16 53 57 183
ucsc_cell_browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets 2018-09-11 https://cells.ucsc.edu/ 1.0.0+galaxy1 ucsc-cell-browser 1.2.8 To update Transcriptomics ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 178 181 965 975 0 0 0 0 0 0 0 0 178 537 965 2905
-unipept unipept Unipept retrieves metaproteomics information 2015-04-03 https://github.com/galaxyproteomics/tools-galaxyp 4.5.1 python To update Proteomics Prediction and recognition, Visualisation Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows Proteomics, Proteogenomics, Biodiversity, Workflows galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 257 270 4900 5146 81 81 251 251 29 29 1069 1069 367 1114 6220 18906
-uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format 2016-03-08 2.4.0 requests To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 230 266 1488 1596 0 0 0 0 35 35 743 743 265 831 2231 6801
+unipept unipept Unipept retrieves metaproteomics information 2015-04-03 https://github.com/galaxyproteomics/tools-galaxyp 4.5.1 python To update Proteomics Prediction and recognition, Visualisation Prediction and recognition, Visualisation Proteomics, Proteogenomics, Biodiversity, Workflows Proteomics, Proteogenomics, Biodiversity, Workflows galaxyp https://unipept.ugent.be/apidocs https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept unipept Unipept Metaproteomics data analysis with a focus on interactive data visualizations. 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 257 270 4900 5146 81 81 251 251 29 29 1069 1069 367 1114 6220 18906
+uniprotxml_downloader uniprotxml_downloader Download UniProt proteome in XML or fasta format 2016-03-08 https://www.uniprot.org/help/programmatic_access 2.5.0 requests To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 230 266 1488 1596 0 0 0 0 35 35 743 743 265 831 2231 6801
upload_roi_and_measures_to_omero uploadROIandMeasuresToOMERO Upload the ROI coordinates and the measurements to the omero server 2022-01-18 0.0.5 omero-py 5.11.1 To update Imaging lldelisle https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
validate_fasta_database validate_fasta_database runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks. 2017-09-14 0.1.5 validate-fasta-database 1.0 To update Fasta Manipulation, Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 38 38 112 112 0 0 0 0 0 0 0 0 38 114 112 336
varscan_vaf varscan_vaf Compute variant allele frequency in vcf files generated by varscan. 2022-11-28 http://artbio.fr 0.1 python To update Variant Analysis artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
@@ -1451,10 +1454,10 @@ vmd vmd is a package for visualizing and analyzing trajectories from molecular
xmlstarlet xmlstarlet Tool to convert a xml file from one metadata standard to another 2021-10-18 1.6.1 xmlstarlet To update Convert Formats ecology https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 17 17 59 59 0 0 0 0 0 0 0 0 17 51 59 177
xpore xpore_dataprep, xpore_diffmod Identification and quantification of differential RNA modifications from direct RNA sequencing 2021-05-26 https://github.com/GoekeLab/xpore 2.1+galaxy0 xpore 2.1 To update Nanopore artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
xtb_molecular_optimization xtb_molecular_optimization Performs semiempirical molecular optimization. 2023-08-24 https://github.com/grimme-lab/xtb 6.6.1 xtb To update Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/xtb https://github.com/RECETOX/galaxytools/tree/master/tools/xtb 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 143 143 0 0 0 0 0 0 0 0 4 12 143 429
-yac_clipper yac Clips 3' adapters for small RNA sequencing reads. 2015-06-17 http://artbio.fr 2.5.1 python To update RNA, Fastq Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+yac_clipper yac Clips 3' adapters for small RNA sequencing reads. 2015-06-17 http://artbio.fr 2.5.1 python To update RNA, Fastq Manipulation artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch 2015-08-28 http://proteowizard.sourceforge.net/ 3.0.21142 bumbershoot 3_0_21142_0e4f4a4 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 21 32 1186 1356 0 0 0 0 0 0 0 0 21 74 1186 3728
cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots Statistical and computational tools for analyzing mass spectrometry imaging datasets 2018-10-01 http://cardinalmsi.org 3.4.3 bioconductor-cardinal 3.4.3 Up-to-date Proteomics, Metabolomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal 0 9 11 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 11 9 0 663 713 41875 50702 1 1 12 12 231 231 7512 7512 895 2735 49399 157024
- msstats MSstats tool for analyzing mass spectrometry proteomic datasets 2020-07-25 https://github.com/MeenaChoi/MSstats 4.0.0 bioconductor-msstats 4.10.0 To update Proteomics Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression Proteomics, Proteomics experiment, Protein expression galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 559 559 2353 2353 211 211 1122 1122 35 35 1091 1091 805 2415 4566 13698
+ msstats MSstats tool for analyzing mass spectrometry proteomic datasets 2020-07-25 https://github.com/MeenaChoi/MSstats 4.0.0 bioconductor-msstats 4.14.0 To update Proteomics Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling Proteomics, Proteomics experiment, Protein expression Proteomics, Proteomics experiment, Protein expression galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats msstatstmt MSstatsTMT Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 559 559 2353 2353 211 211 1122 1122 35 35 1091 1091 805 2415 4566 13698
pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample Semi-supervised learning and scoring of OpenSWATH results. 2015-02-06 https://github.com/PyProphet/pyprophet 2.1.4 pyprophet 2.2.5 To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet 0 5 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 6 6 0 150 150 2626 2626 0 0 0 0 9 9 609 609 159 477 3235 9705
ZeissLMDconverter Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems 2024-06-29 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 2.0.4 shapely To update Proteomics galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 4 4 0 0 0 0 0 0 0 0 1 3 4 12
aquainfra_importer A data source tool for downloading datasets via the AquaINFRA Interaction Platform. 2024-05-14 https://github.com/AquaINFRA/galaxy 1.0 To update Ecology ecology https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 9 75 75 0 0 0 0 0 0 0 0 9 27 75 225
diff --git a/communities/all/resources/tools_wordcloud.png b/communities/all/resources/tools_wordcloud.png
index 46949afe..06b06335 100644
Binary files a/communities/all/resources/tools_wordcloud.png and b/communities/all/resources/tools_wordcloud.png differ
diff --git a/communities/all/resources/tutorials.json b/communities/all/resources/tutorials.json
index 2d4b3380..0b36d2c7 100644
--- a/communities/all/resources/tutorials.json
+++ b/communities/all/resources/tutorials.json
@@ -8,20 +8,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/tutorial.json",
- "contributions": {
- "authorship": [
- "natefoo",
- "hexylena"
- ],
- "reviewing": [
- "hexylena",
- "lldelisle",
- "natefoo",
- "nsoranzo",
- "martenson",
- "shiltemann"
- ]
- },
"contributors": [
{
"email": "nate@bx.psu.edu",
@@ -62,138 +48,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "ch",
- "email": "lucille.delisle@epfl.ch",
- "id": "lldelisle",
- "joined": "2019-08",
- "location": {
- "country": "CH",
- "lat": 46.52,
- "lon": 6.56
- },
- "name": "Lucille Delisle",
- "orcid": "0000-0002-1964-4960",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
- },
- {
- "email": "nate@bx.psu.edu",
- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
- "id": "martenson",
- "joined": "2017-09",
- "location": {
- "country": "USA",
- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/admin/tutorials/systemd-supervisor",
@@ -211,7 +65,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2023-04-16",
- "pageviews": 6179062,
+ "pageviews": 6202042,
"pub_date": "2019-01-28",
"short_id": "S00023",
"short_tools": [],
@@ -243,7 +97,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 153,
- "visitors": 2242499
+ "visitors": 2253323
},
{
"admin_install": {
@@ -254,22 +108,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/tutorial.json",
- "contributions": {
- "authorship": [
- "natefoo",
- "slugger70"
- ],
- "reviewing": [
- "martenson",
- "nsoranzo",
- "hexylena",
- "bgruening",
- "mvdbeek",
- "natefoo",
- "slugger70",
- "shiltemann"
- ]
- },
"contributors": [
{
"email": "nate@bx.psu.edu",
@@ -292,168 +130,6 @@
"orcid": "0000-0002-6100-4385",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
- "id": "martenson",
- "joined": "2017-09",
- "location": {
- "country": "USA",
- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "id": "mvdbeek",
- "joined": "2018-06",
- "name": "Marius van den Beek",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
- },
- {
- "email": "nate@bx.psu.edu",
- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
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- "joined": "2017-09",
- "linkedin": "shiltemann",
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- "lat": 51.912,
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
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@@ -471,7 +147,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2022-03-01",
- "pageviews": 6179062,
+ "pageviews": 6202042,
"pub_date": "2019-01-28",
"short_id": "S00028",
"short_tools": [],
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"video_view": 0,
"visit_duration": 153,
- "visitors": 2242499
+ "visitors": 2253323
},
{
"abbreviations": {
@@ -1147,7 +823,7 @@
"Have an understanding of how Galaxy's Ansible roles are structured and interact with one another",
"Be able to use an Ansible playbook to install different flavors of Galaxy for different purposes"
],
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"video_versions": 3,
"video_view": 0,
"visit_duration": 257,
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- "natefoo",
- "slugger70"
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@@ -1352,114 +1013,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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@@ -1477,7 +1030,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2022-03-01",
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"pub_date": "2019-04-26",
"short_id": "S00012",
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"visit_duration": 153,
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@@ -1520,23 +1073,6 @@
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@@ -1586,163 +1122,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
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- "location": {
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- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
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- "email": "nate@bx.psu.edu",
- "id": "natefoo",
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- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
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@@ -1760,7 +1139,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2023-04-16",
- "pageviews": 6179062,
+ "pageviews": 6202042,
"pub_date": "2019-01-28",
"short_id": "S00019",
"short_tools": [],
@@ -1792,7 +1171,7 @@
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"video_view": 0,
"visit_duration": 153,
- "visitors": 2242499
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},
{
"abbreviations": {
@@ -2014,7 +1393,7 @@
"Setup cleanups",
"Learn what to back up and how to recover"
],
- "pageviews": 6179642,
+ "pageviews": 6202627,
"pub_date": "2019-01-31",
"questions": [
"How can I back up my Galaxy?",
@@ -2071,8 +1450,8 @@
"video": true,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 760,
- "visitors": 2242925
+ "visit_duration": 768,
+ "visitors": 2253753
},
{
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@@ -2447,7 +1826,7 @@
"Configure your Galaxy to serve Interactive Tools using an Ansible Playbook",
"Start, run, and use an Interactive Tool"
],
- "pageviews": 6182125,
+ "pageviews": 6205108,
"pub_date": "2020-02-27",
"questions": [
"What are Galaxy Interactive Tools?",
@@ -2514,8 +1893,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 319,
- "visitors": 2244485,
+ "visit_duration": 318,
+ "visitors": 2255312,
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},
{
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"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json",
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@@ -2586,226 +1946,6 @@
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{
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"Generation",
"Sequence alignment",
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"data_manager_fetch_genome_all_fasta_dbkey",
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@@ -5376,7 +3527,7 @@
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@@ -5759,7 +3676,7 @@
"be familiar with configuring Galaxy to use an upstream (proxy) authentication provider",
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],
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@@ -6061,7 +3820,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2021-04-06",
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+ "pageviews": 6202042,
"pub_date": "2019-01-31",
"short_id": "S00009",
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+ "visitors": 2253323
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@@ -6103,26 +3862,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/tutorial.json",
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@@ -6205,217 +3944,6 @@
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
+ "elixir_node": "de",
+ "email": "kuntzm@informatik.uni-freiburg.de",
+ "id": "mira-miracoli",
+ "joined": "2022-07",
+ "matrix": "mira-miracoli:matrix.org",
+ "name": "Mira Kuntz",
+ "orcid": "0000-0003-4302-5091",
+ "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
+ "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
},
{
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@@ -7097,7 +4351,7 @@
"Use an Ansible playbook for all of the above.",
"Monitor a Celery task using the Flower dashboard"
],
- "pageviews": 3358344,
+ "pageviews": 3381326,
"pub_date": "2022-07-16",
"questions": null,
"requirements": [
@@ -7145,8 +4399,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 250,
- "visitors": 1385416,
+ "visit_duration": 249,
+ "visitors": 1395448,
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{
@@ -7158,21 +4412,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/tutorial.json",
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- "shiltemann"
- ]
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@@ -7253,119 +4492,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "fediverse": "https://mstdn.science/@shiltemann",
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@@ -7383,7 +4509,7 @@
"license": "CC-BY-4.0",
"logo": "assets/images/gat.png",
"mod_date": "2022-06-16",
- "pageviews": 6179062,
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"short_id": "S00008",
"short_tools": [],
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"visit_duration": 153,
- "visitors": 2242499
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@@ -7428,25 +4554,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json",
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- "TKlingstrom"
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@@ -7476,244 +4583,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "twitter": "bjoerngruening",
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- "matrix": "TKlingstrom:matrix.org",
- "name": "Tomas Klingstr\u00f6m",
- "orcid": "0000-0002-9504-1352",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/",
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"dir": "topics/admin/tutorials/monitoring",
@@ -7743,7 +4612,7 @@
"Setup Grafana",
"Create several charts"
],
- "pageviews": 6184203,
+ "pageviews": 6207186,
"pub_date": "2019-01-31",
"questions": [
"How to monitor Galaxy with Telegraf",
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"video_versions": 1,
"video_view": 0,
"visit_duration": 204,
- "visitors": 2245214
+ "visitors": 2256041
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{
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@@ -8137,7 +5006,7 @@
"Learn the Galaxy user/group management and assign Quotas.",
"Understand the Role Based Access Control (RBAC) of Galaxy."
],
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"visit_duration": 153,
- "visitors": 2242499,
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"api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tool-management/tutorial.json",
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{
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@@ -8307,255 +5155,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
"twitter": "NicolaSoranzo",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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"visit_duration": 377,
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@@ -8936,26 +5365,6 @@
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@@ -9034,200 +5443,6 @@
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@@ -9253,7 +5468,7 @@
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"Setup and start the Galaxy reports app."
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@@ -11262,7 +6615,7 @@
"Configure galaxy and install a FTP server.",
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],
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+ "pageviews": 1507,
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],
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@@ -13230,7 +7864,7 @@
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- "Sequence composition calculation"
+ "Sequence composition calculation",
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],
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"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
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@@ -17477,18 +10521,18 @@
"assemble some paired end reads using Velvet",
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],
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],
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"short_tools": [
- "fastqc",
- "velvetg",
- "multiqc",
"quast",
+ "multiqc",
"velveth",
+ "fastqc",
+ "velvetg",
"fastq_paired_end_interlacer"
],
"slides": true,
@@ -17540,11 +10584,6 @@
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}
]
},
@@ -17570,6 +10609,10 @@
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},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -17625,10 +10668,6 @@
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},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -17675,11 +10714,6 @@
"url": "https://usegalaxy.eu",
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},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -17724,6 +10758,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -17779,10 +10817,6 @@
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{
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{
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@@ -17876,6 +10905,10 @@
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{
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"0.68",
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{
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"0.72",
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]
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{
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@@ -18239,6 +11258,10 @@
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},
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{
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{
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@@ -18343,13 +11362,6 @@
"1.2.10.2"
]
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{
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@@ -18394,6 +11406,10 @@
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},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -18447,10 +11463,6 @@
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{
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@@ -18496,11 +11508,6 @@
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{
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@@ -18545,6 +11552,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -18649,13 +11656,6 @@
"1.2.10.3"
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{
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"state": "missing"
@@ -18700,6 +11700,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -18851,6 +11846,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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@@ -18972,8 +11962,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -19016,6 +12006,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -19070,10 +12064,6 @@
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{
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@@ -19126,11 +12116,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -19176,6 +12161,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -19236,10 +12225,6 @@
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{
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@@ -19286,11 +12271,6 @@
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{
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@@ -19299,9 +12279,9 @@
"5.0.2+galaxy1",
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"5.0.2+galaxy4",
+ "5.0.2+galaxy2",
"5.0.2+galaxy5",
- "5.0.2+galaxy3",
- "5.0.2+galaxy2"
+ "5.0.2+galaxy3"
]
},
{
@@ -19344,6 +12324,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -19398,10 +12382,6 @@
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{
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"state": "exact",
@@ -19438,8 +12418,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -19452,11 +12432,6 @@
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},
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- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -19517,7 +12492,7 @@
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"video_view": 0,
"visit_duration": 322,
- "visitors": 2272160,
+ "visitors": 2283088,
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@@ -19673,7 +12648,7 @@
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+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Intro to Genome Assembly",
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{
@@ -20445,17 +13420,16 @@
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"Genome assembly",
- "De-novo assembly",
- "Mapping assembly",
"Sequence assembly validation",
- "Cross-assembly",
"Transcriptome assembly",
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+ "De-novo assembly"
],
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- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
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@@ -20494,7 +13468,7 @@
"Assemble a Genome with PacBio data",
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],
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+ "pageviews": 4880,
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"questions": [
"How to perform a genome assembly with PacBio data ?",
@@ -20502,10 +13476,10 @@
],
"short_id": "T00033",
"short_tools": [
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- "quast",
"busco",
- "fasta-stats"
+ "fasta-stats",
+ "flye",
+ "quast"
],
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@@ -20516,11 +13490,6 @@
"url": "https://usegalaxy.eu",
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},
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -20577,6 +13546,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -20632,10 +13605,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -20682,11 +13651,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
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"url": "https://usegalaxy.no/",
@@ -20731,6 +13695,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
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@@ -20787,10 +13755,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -20837,11 +13801,6 @@
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{
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"state": "exact",
@@ -20887,6 +13846,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -20919,10 +13882,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
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@@ -20945,10 +13908,6 @@
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{
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"state": "missing"
@@ -20996,11 +13955,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "5.2.2+galaxy0"
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{
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"state": "exact",
@@ -21046,6 +14000,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -21099,10 +14057,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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{
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@@ -21150,11 +14104,6 @@
"state": "exact",
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},
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- "version": "5.2.2+galaxy2"
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{
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"state": "exact",
@@ -21200,6 +14149,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -21257,10 +14210,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -21306,11 +14255,6 @@
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- "version": "2.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -21356,6 +14300,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -21380,8 +14328,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
- "5.2.0+galaxy1"
+ "5.2.0+galaxy1",
+ "5.0.2+galaxy0"
]
},
{
@@ -21419,10 +14367,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -21461,8 +14405,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -21475,11 +14419,6 @@
"state": "exact",
"version": "5.0.2+galaxy3"
},
- {
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- "state": "exact",
- "version": "5.0.2+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -21537,8 +14476,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 127,
- "visitors": 3553,
+ "visit_duration": 129,
+ "visitors": 3567,
"workflows": [
{
"creators": [
@@ -21669,7 +14608,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPacBio reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Flye\"];\n 0 -->|output| 2;\n d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a[\"Output\\nFlye on input dataset(s): assembly info\"];\n 2 --> d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a;\n style d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a stroke:#2c3143,stroke-width:4px;\n c8f96c22-e06e-4fec-bbfa-d993b7b103eb[\"Output\\nFlye on input dataset(s): consensus\"];\n 2 --> c8f96c22-e06e-4fec-bbfa-d993b7b103eb;\n style c8f96c22-e06e-4fec-bbfa-d993b7b103eb stroke:#2c3143,stroke-width:4px;\n a288fb93-5aa5-4231-89e4-958c57106978[\"Output\\nFlye on input dataset(s): graphical fragment assembly\"];\n 2 --> a288fb93-5aa5-4231-89e4-958c57106978;\n style a288fb93-5aa5-4231-89e4-958c57106978 stroke:#2c3143,stroke-width:4px;\n 0e064181-5cd4-42c8-98f9-fe417303956c[\"Output\\nFlye on input dataset(s): assembly graph\"];\n 2 --> 0e064181-5cd4-42c8-98f9-fe417303956c;\n style 0e064181-5cd4-42c8-98f9-fe417303956c stroke:#2c3143,stroke-width:4px;\n 3[\"Fasta Statistics\"];\n 1 -->|output| 3;\n 4[\"Busco\"];\n 1 -->|output| 4;\n 5[\"Fasta Statistics\"];\n 2 -->|consensus| 5;\n 6[\"Quast\"];\n 1 -->|output| 6;\n 2 -->|consensus| 6;\n bea191cb-f88d-4103-b8fa-b3683d77cc93[\"Output\\nQuast on input dataset(s): HTML report\"];\n 6 --> bea191cb-f88d-4103-b8fa-b3683d77cc93;\n style bea191cb-f88d-4103-b8fa-b3683d77cc93 stroke:#2c3143,stroke-width:4px;\n 7[\"Busco\"];\n 2 -->|consensus| 7;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Genome Assembly using PacBio data",
"outputs": [
{
@@ -21978,25 +14917,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fasta_stats\n owner: iuc\n revisions: 9c620a950d3a\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: spades\n owner: nml\n revisions: b7829778729f\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: velvetoptimiser\n owner: simon-gladman\n revisions: 37d88f41c810\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "mblue9"
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"contributors": [
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@@ -22070,187 +14990,6 @@
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- "email": "simon.gladman@unimelb.edu.au",
- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
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- "name": "Niall Beard",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
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- {
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- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/assembly/tutorials/debruijn-graph-assembly",
@@ -22294,7 +15033,7 @@
"Compare this assembly with those we did in the basic tutorial",
"Perform an assembly using the SPAdes assembler."
],
- "pageviews": 6187905,
+ "pageviews": 6210900,
"pub_date": "2017-05-24",
"questions": [
"What are the factors that affect genome assembly?",
@@ -22302,9 +15041,9 @@
],
"short_id": "T00031",
"short_tools": [
- "spades",
+ "fasta-stats",
"velvetoptimiser",
- "fasta-stats"
+ "spades"
],
"slides": true,
"slides_recordings": false,
@@ -22371,6 +15110,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -22426,10 +15169,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -22476,11 +15215,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -22525,6 +15259,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -22582,10 +15320,6 @@
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{
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{
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"state": "exact",
@@ -22684,6 +15410,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -22738,10 +15468,6 @@
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},
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{
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"state": "inexact",
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},
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- "state": "exact",
- "version": "3.12.0+galaxy1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -22841,6 +15562,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -22897,10 +15622,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -22944,10 +15665,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -22999,8 +15716,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 303,
- "visitors": 2247964,
+ "visit_duration": 302,
+ "visitors": 2258800,
"workflows": [
{
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@@ -23098,7 +15815,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Debruijn Graph",
"outputs": [
{
@@ -23374,24 +16091,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
- "contributions": {
- "authorship": [
- "nekrut",
- "delphine-l",
- "hexylena"
- ],
- "reviewing": [
- "bebatut",
- "shiltemann",
- "bgruening",
- "hexylena",
- "abretaud",
- "nsoranzo",
- "nekrut",
- "njall",
- "mblue9"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -23438,191 +16137,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
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- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
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- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
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- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "email": "anton@nekrut.org",
- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
- },
- {
- "id": "mblue9",
- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/assembly/tutorials/ecoli_comparison",
@@ -23632,11 +16146,11 @@
"topic_3301"
],
"edam_operation": [
+ "Sequence visualisation",
"Read mapping",
"Mapping",
- "Genome visualisation",
"Sequence alignment",
- "Sequence visualisation"
+ "Genome visualisation"
],
"edam_topic": [
"Sequence assembly",
@@ -23667,7 +16181,7 @@
"Perform sequence comparison to locate rearrangements",
"Identify genes located in deletions"
],
- "pageviews": 12347,
+ "pageviews": 12361,
"pub_date": "2018-06-14",
"questions": [
"I just assembled a genome. How does it compare with already sequenced genomes?",
@@ -23684,33 +16198,33 @@
],
"short_id": "T00032",
"short_tools": [
+ "cat1",
+ "tp_sort_header_tool",
+ "Filter1",
+ "Cut1",
+ "mergeCols1",
+ "fasta_compute_length",
+ "Grep1",
+ "tp_replace_in_line",
"bedtools_complementbed",
- "datamash_ops",
- "tp_cat",
"tp_replace_in_column",
- "tp_replace_in_line",
+ "tp_cat",
+ "tp_grep_tool",
+ "lastz_wrapper_2",
+ "random_lines1",
+ "datamash_ops",
"jbrowse",
- "tp_sort_header_tool",
- "upload1",
+ "addValue",
+ "circos",
+ "tp_sed_tool",
+ "bedtools_intersectbed",
+ "collapse_dataset",
"circos_aln_to_links",
"circos_interval_to_tiles",
"fasta_filter_by_length",
- "bedtools_sortbed",
- "addValue",
- "random_lines1",
- "Filter1",
- "tp_grep_tool",
"join1",
- "tp_sed_tool",
- "Cut1",
- "collapse_dataset",
- "Grep1",
- "lastz_wrapper_2",
- "cat1",
- "circos",
- "mergeCols1",
- "fasta_compute_length",
- "bedtools_intersectbed"
+ "upload1",
+ "bedtools_sortbed"
],
"slides": false,
"slides_recordings": false,
@@ -23740,6 +16254,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -23795,10 +16313,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -23845,11 +16359,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -23894,6 +16403,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -23946,10 +16459,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -23990,10 +16499,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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- "state": "local"
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{
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"state": "local"
@@ -24036,6 +16541,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -24088,10 +16597,6 @@
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"state": "missing"
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{
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"state": "local"
@@ -24132,10 +16637,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
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- "state": "local"
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{
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"state": "local"
@@ -24178,6 +16679,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -24230,10 +16735,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -24274,10 +16775,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -24320,6 +16817,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -24372,10 +16873,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "local"
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{
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"state": "local"
@@ -24416,10 +16913,6 @@
"server": "https://usegalaxy.eu",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -24462,6 +16955,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -24514,10 +17011,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -24558,10 +17051,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -24604,6 +17093,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -24656,10 +17149,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
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{
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@@ -24700,10 +17189,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -24746,6 +17231,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -24800,10 +17289,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -24850,11 +17335,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
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- "state": "exact",
- "version": "0.1.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -24900,6 +17380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -24954,10 +17438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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@@ -25208,6 +17678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -25262,10 +17736,6 @@
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@@ -25362,6 +17827,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -25467,7 +17932,151 @@
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{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.1.1"
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+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
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+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.1.1"
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "https://galaxytrakr.org/",
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+ "version": "1.1.1"
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+ "server": "http://hyperbrowser.uio.no/hb/",
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
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+ "version": "1.1.1"
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+ {
+ "server": "https://usegalaxy.eu",
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
"servers": [
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@@ -25670,6 +18125,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -25723,10 +18182,6 @@
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},
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{
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@@ -25773,11 +18228,6 @@
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- "state": "exact",
- "version": "1.0.0"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -25822,6 +18272,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -25877,10 +18331,6 @@
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{
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@@ -25930,15 +18380,6 @@
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- "1.0.2",
- "1.0.4"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -25991,6 +18432,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -26043,10 +18488,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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},
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- "state": "exact",
- "version": "1.1"
- },
{
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"state": "exact",
@@ -26147,6 +18583,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -26199,10 +18639,6 @@
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{
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@@ -26247,11 +18683,6 @@
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- "version": "1.2"
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{
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"state": "exact",
@@ -26297,6 +18728,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -26351,10 +18786,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
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{
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@@ -26392,8 +18823,8 @@
"server": "https://usegalaxy.cz/",
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- "1.04.22+galaxy0"
+ "1.04.22+galaxy0",
+ "1.04.15+galaxy0"
]
},
{
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{
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"state": "exact",
@@ -26451,6 +18877,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -26503,10 +18933,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- },
{
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@@ -26550,13 +18976,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
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{
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"state": "missing"
@@ -26603,6 +19022,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -26660,16 +19083,12 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- },
{
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- "2.31.1+galaxy0"
+ "2.31.1+galaxy0",
+ "2.30.0+galaxy1"
]
},
{
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- "2.30.0+galaxy1",
- "2.31.1+galaxy0",
- "2.29.0"
- ]
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{
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"state": "inexact",
@@ -26778,6 +19186,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
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@@ -26835,10 +19247,6 @@
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{
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@@ -26884,9 +19292,9 @@
"2.29.2",
"2.30.0",
"2.30.0+galaxy1",
- "2.27.1+galaxy1",
"2.19.0",
- "2.29.0"
+ "2.29.0",
+ "2.27.1+galaxy1"
]
},
{
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{
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@@ -26954,6 +19351,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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"server": "https://galaxytrakr.org/",
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+ "2.30.0",
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]
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{
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{
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+ "2.29.2",
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"2.29.0",
"2.19.0",
@@ -27070,23 +19467,12 @@
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{
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"versions": [
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"2.30.0",
+ "2.29.2",
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]
},
@@ -27130,6 +19516,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -27186,10 +19576,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -27242,11 +19628,6 @@
"0.69.8+galaxy10"
]
},
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- "state": "exact",
- "version": "0.69.8+galaxy7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -27292,6 +19673,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -27348,10 +19733,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -27400,11 +19781,6 @@
"state": "exact",
"version": "0.69.8+galaxy7"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.69.8+galaxy7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -27450,6 +19826,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -27502,10 +19882,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -27546,10 +19922,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -27592,6 +19964,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -27649,10 +20025,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -27699,11 +20071,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -27749,6 +20116,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -27812,10 +20183,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -27864,11 +20231,6 @@
"state": "exact",
"version": "1.16.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -27918,6 +20280,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -27943,8 +20309,8 @@
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -27978,10 +20344,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -28031,21 +20393,13 @@
"state": "exact",
"version": "4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -28088,6 +20442,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -28144,10 +20502,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -28197,14 +20551,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -28250,6 +20596,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -28302,10 +20652,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -28346,10 +20692,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -28431,7 +20773,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 180,
- "visitors": 6194,
+ "visitors": 6204,
"workflows": [
{
"creators": [],
@@ -28621,7 +20963,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Collapse Collection\"];\n 6 -->|output| 10;\n 11[\"Text transformation\"];\n 7 -->|output| 11;\n 12[\"Add column\"];\n 8 -->|out_file1| 12;\n 13[\"LASTZ\"];\n 9 -->|output| 13;\n 3 -->|output| 13;\n 14[\"random_lines1\"];\n 10 -->|output| 14;\n 15[\"Filter\"];\n 10 -->|output| 15;\n 16[\"Search in textfiles\"];\n 11 -->|output| 16;\n 17[\"Concatenate datasets\"];\n 11 -->|output| 17;\n 9 -->|output| 17;\n 18[\"Cut\"];\n 12 -->|out_file1| 18;\n 19[\"Text transformation\"];\n 13 -->|output| 19;\n 2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 20[\"Datamash\"];\n 15 -->|out_file1| 20;\n 21[\"Compute sequence length\"];\n 17 -->|out_file1| 21;\n 22[\"Collapse Collection\"];\n 18 -->|out_file1| 22;\n 23[\"Merge Columns\"];\n 19 -->|output| 23;\n 24[\"Select\"];\n 20 -->|out_file| 24;\n 25[\"Sort\"];\n 21 -->|output| 25;\n 26[\"Collapse Collection\"];\n 23 -->|out_file1| 26;\n 27[\"Cut\"];\n 26 -->|output| 27;\n 28[\"Cut\"];\n 26 -->|output| 28;\n 29[\"Concatenate datasets\"];\n 27 -->|out_file1| 29;\n 28 -->|out_file1| 29;\n 3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 30[\"SortBED\"];\n 29 -->|out_file1| 30;\n 31[\"ComplementBed\"];\n 25 -->|outfile| 31;\n 30 -->|output| 31;\n 32[\"Filter\"];\n 31 -->|output| 32;\n 33[\"Filter\"];\n 32 -->|out_file1| 33;\n 34[\"Intersect intervals\"];\n 33 -->|out_file1| 34;\n 22 -->|output| 34;\n 35[\"Join two Datasets\"];\n 34 -->|output| 35;\n 1 -->|output| 35;\n 4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Filter sequences by length\"];\n 0 -->|output| 5;\n 6[\"LASTZ\"];\n 2 -->|output| 6;\n 0 -->|output| 6;\n 7[\"Collapse Collection\"];\n 3 -->|output| 7;\n 8[\"Select\"];\n 4 -->|output| 8;\n 9[\"Text transformation\"];\n 5 -->|output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Ecoli Comparison",
"outputs": [],
"parent_id": "assembly/ecoli_comparison",
@@ -28701,28 +21043,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: quast\n owner: iuc\n revisions: 72472698a2df\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
- "contributions": {
- "authorship": [
- "delphine-l",
- "astrovsky01",
- "gallardoalba",
- "pickettbd",
- "abueg",
- "nekrut"
- ],
- "reviewing": [
- "hexylena",
- "bgruening",
- "teresa-m",
- "abueg",
- "gallardoalba",
- "shiltemann",
- "annasyme",
- "bebatut",
- "delphine-l",
- "nekrut"
- ]
- },
"contributors": [
{
"email": "delphine.lariviere@galaxy.org",
@@ -28771,183 +21091,6 @@
"twitter": "llabueg",
"url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
},
- {
- "email": "anton@nekrut.org",
- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
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- "gallantries",
- "by-covid",
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- "elixir-converge"
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- "elixir_node": "nl",
- "former_affiliations": [
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- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
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- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
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- "name": "Linelle Abueg",
- "orcid": "0000-0002-6879-3954",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
- "twitter": "llabueg",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
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- "former_affiliations": [
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- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "joined": "2017-09",
- "name": "Anna Syme",
- "orcid": "0000-0002-9906-0673",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
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- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "delphine.lariviere@galaxy.org",
- "id": "delphine-l",
- "joined": "2017-09",
- "name": "Delphine Lariviere",
- "orcid": "0000-0001-6421-3484",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
{
"email": "anton@nekrut.org",
"id": "nekrut",
@@ -28959,8 +21102,8 @@
],
"dir": "topics/assembly/tutorials/vgp_workflow_training",
"edam_operation": [
- "Visualisation",
- "Sequence assembly validation"
+ "Sequence assembly validation",
+ "Visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -28969,7 +21112,6 @@
"MISSISSIPPI",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -28997,7 +21139,7 @@
"Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
"Evaluate the quality of the assembly"
],
- "pageviews": 3307,
+ "pageviews": 3315,
"pub_date": "2022-04-06",
"questions": [
"What combination of tools can produce the highest quality assembly of vertebrate genomes?",
@@ -29051,11 +21193,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -29102,6 +21239,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -29157,10 +21298,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -29207,11 +21344,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -29256,6 +21388,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -29310,10 +21446,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -29350,8 +21482,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -29364,11 +21496,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
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- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -29424,7 +21551,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 172,
- "visitors": 2309,
+ "visitors": 2317,
"zenodo_link": "https://zenodo.org/record/5887339"
},
{
@@ -29521,22 +21648,6 @@
},
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- "abretaud",
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{
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@@ -29545,215 +21656,28 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
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- "twitter": "abretau",
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- "deNBI",
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- "Genome annotation",
- "Analysis",
- "Coding region prediction",
- "Genome visualisation",
- "Sequence assembly",
"Genome indexing",
- "Scatter plot plotting",
+ "Read alignment",
+ "Genome annotation",
"Genome assembly",
- "Sequence alignment",
- "Mapping assembly",
- "Sequence assembly visualisation",
"Gene prediction",
- "Read mapping",
+ "Sequence assembly visualisation",
+ "Analysis",
"Cross-assembly",
- "Generation"
+ "Coding region prediction",
+ "Generation",
+ "Read mapping",
+ "Mapping assembly",
+ "Sequence alignment",
+ "Scatter plot plotting",
+ "Sequence assembly",
+ "Genome visualisation",
+ "Box-Whisker plot plotting"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -29767,7 +21691,6 @@
"GalaxyTrakr",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -29790,7 +21713,7 @@
"Annotate the assembly and view",
"Map reads to the assembly and view"
],
- "pageviews": 10229,
+ "pageviews": 10254,
"pub_date": "2020-12-04",
"questions": [
"How can we assemble a chloroplast genome?"
@@ -29824,16 +21747,16 @@
],
"short_id": "T00030",
"short_tools": [
+ "bandage_info",
+ "bandage_image",
"fasta-stats",
- "prokka",
+ "bwa_mem",
"nanoplot",
+ "prokka",
"pilon",
- "jbrowse",
"flye",
- "bandage_info",
"upload1",
- "bwa_mem",
- "bandage_image"
+ "jbrowse"
],
"slides": false,
"slides_recordings": false,
@@ -29861,11 +21784,6 @@
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"usegalaxy": false
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -29900,6 +21818,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -29955,10 +21877,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -30005,11 +21923,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -30054,6 +21967,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"state": "exact",
@@ -30215,6 +22115,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -30251,10 +22155,11 @@
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"2.8.2+galaxy0",
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+ "2.9+galaxy0",
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+ "2.9.5+galaxy1"
]
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"versions": [
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"2.9.1+galaxy0",
"2.8.2+galaxy0",
"2.9+galaxy0",
+ "2.6",
"2.3.7",
"2.3.5",
"2.8.3+galaxy0"
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"2.8.2+galaxy0",
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"2.8.3+galaxy0",
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"2.3.7",
"2.8.3+galaxy0",
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]
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -30470,10 +22363,6 @@
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"state": "inexact",
@@ -30581,6 +22461,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
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@@ -30639,10 +22523,6 @@
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@@ -30714,8 +22589,8 @@
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"1.12.0",
+ "1.14.5",
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]
},
@@ -30749,6 +22624,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
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@@ -30806,10 +22685,6 @@
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@@ -30910,6 +22780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -30934,8 +22808,8 @@
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"versions": [
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"0.8.1+galaxy4",
+ "0.8.1+galaxy0+galaxy0",
"2022.09+galaxy4"
]
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@@ -30975,10 +22849,6 @@
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{
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@@ -31028,11 +22898,6 @@
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{
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"state": "exact",
@@ -31078,6 +22943,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -31102,9 +22971,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
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+ "2022.09+galaxy2",
"0.8.1+galaxy0+galaxy0",
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+ "0.8.1+galaxy2"
]
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{
@@ -31137,16 +23006,12 @@
"server": "http://galaxy.interactomix.com/",
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+ "2022.09+galaxy2",
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@@ -31190,11 +23055,6 @@
"state": "exact",
"version": "0.8.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -31240,6 +23100,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -31297,10 +23161,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -31346,14 +23206,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0",
- "1.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -31399,6 +23251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -31456,10 +23312,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -31505,11 +23357,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -31555,6 +23402,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -31618,10 +23469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -31670,17 +23517,6 @@
"state": "exact",
"version": "1.16.4+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.16.9+galaxy0",
- "1.16.11+galaxy1",
- "1.16.10+galaxy0",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -31730,6 +23566,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -31790,10 +23630,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -31842,11 +23678,6 @@
"state": "exact",
"version": "1.16.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -31892,6 +23723,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -31951,10 +23786,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -32003,11 +23834,6 @@
"state": "exact",
"version": "1.28.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -32053,6 +23879,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -32106,10 +23936,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -32153,11 +23979,6 @@
"state": "exact",
"version": "1.20.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.20.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -32203,6 +24024,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -32255,10 +24080,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -32299,10 +24120,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -32368,7 +24185,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 171,
- "visitors": 6438,
+ "visitors": 6459,
"workflows": [
{
"creators": [],
@@ -32511,7 +24328,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Flye assembly\"];\n 1 -->|output| 4;\n 5[\"NanoPlot\"];\n 1 -->|output| 5;\n 6[\"Map with BWA-MEM\"];\n 0 -->|output| 6;\n 4 -->|consensus| 6;\n 7[\"Fasta Statistics\"];\n 4 -->|consensus| 7;\n 8[\"Bandage Info\"];\n 4 -->|assembly_gfa| 8;\n 9[\"Bandage Image\"];\n 4 -->|assembly_gfa| 9;\n 10[\"pilon\"];\n 6 -->|bam_output| 10;\n 4 -->|consensus| 10;\n 11[\"Fasta Statistics\"];\n 10 -->|output_fasta| 11;\n 12[\"Map with BWA-MEM\"];\n 2 -->|output| 12;\n 10 -->|output_fasta| 12;\n 13[\"Map with BWA-MEM\"];\n 3 -->|output| 13;\n 10 -->|output_fasta| 13;\n 14[\"Prokka\"];\n 10 -->|output_fasta| 14;\n 15[\"JBrowse\"];\n 10 -->|output_fasta| 15;\n 12 -->|bam_output| 15;\n 13 -->|bam_output| 15;\n 16[\"JBrowse\"];\n 10 -->|output_fasta| 16;\n 14 -->|out_gff| 16;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Chloroplast-genome-assembly-and-annotation",
"outputs": [
{
@@ -33856,14 +25673,14 @@
"topic_3301"
],
"edam_operation": [
- "Visualisation",
- "Statistical calculation",
"Sequencing quality control",
+ "Sequence composition calculation",
+ "Visualisation",
+ "Sequence contamination filtering",
"Genome assembly",
"Sequence assembly validation",
- "Sequence composition calculation",
"Sequence assembly visualisation",
- "Sequence contamination filtering"
+ "Statistical calculation"
],
"edam_topic": [
"Sequence assembly",
@@ -33875,7 +25692,6 @@
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -33923,7 +25739,7 @@
"Run tools to assess the quality of an assembly",
"Understand the outputs of tools to assess the quality of an assembly"
],
- "pageviews": 11786,
+ "pageviews": 11854,
"pub_date": "2021-03-24",
"questions": [
"How to check the quality of the MiSeq data?",
@@ -33947,13 +25763,13 @@
],
"short_id": "T00036",
"short_tools": [
- "fastqc",
- "shovill",
- "quast",
"bandage_info",
- "upload1",
"fastp",
- "bandage_image"
+ "bandage_image",
+ "quast",
+ "fastqc",
+ "upload1",
+ "shovill"
],
"slides": false,
"slides_recordings": false,
@@ -33969,11 +25785,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -34025,6 +25836,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -34080,10 +25895,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -34130,11 +25941,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -34179,6 +25985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -34204,8 +26014,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -34242,10 +26052,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -34269,8 +26075,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -34290,12 +26096,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -34308,11 +26114,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -34361,6 +26162,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -34418,10 +26223,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -34471,11 +26272,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -34521,6 +26317,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -34578,10 +26378,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -34630,11 +26426,6 @@
"state": "exact",
"version": "2022.09+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -34680,6 +26471,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -34735,10 +26530,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -34776,11 +26567,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -34793,11 +26584,6 @@
"state": "exact",
"version": "0.23.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -34844,6 +26630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -34898,10 +26688,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -34938,8 +26724,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -34952,11 +26738,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -35002,6 +26783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -35056,10 +26841,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -35093,9 +26874,9 @@
"state": "inexact",
"versions": [
"1.0.4",
+ "0.8.0",
"1.0.4+galaxy0",
- "0.9.0",
- "0.8.0"
+ "0.9.0"
]
},
{
@@ -35108,11 +26889,6 @@
"state": "exact",
"version": "1.1.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -35158,6 +26934,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -35214,10 +26994,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -35251,9 +27027,9 @@
"state": "inexact",
"versions": [
"1.0.4",
+ "0.8.0",
"1.0.4+galaxy0",
- "0.9.0",
- "0.8.0"
+ "0.9.0"
]
},
{
@@ -35266,11 +27042,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -35319,6 +27090,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -35371,10 +27146,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -35415,10 +27186,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -35477,8 +27244,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 222,
- "visitors": 7408,
+ "visit_duration": 221,
+ "visitors": 7454,
"workflows": [
{
"creators": [
@@ -35500,7 +27267,7 @@
"report": null,
"subworkflows": false
},
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+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"]\n 2[label=\"FastQC\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"fastp\"]\n 1 -> 3 [label=\"output\"]\n 0 -> 3 [label=\"output\"]\n k662858b7e6f1438096f040c0eec02a38[color=lightseagreen,label=\"Output\\nfastp_json\"]\n 3 -> k662858b7e6f1438096f040c0eec02a38\n 4[label=\"FastQC\"]\n 1 -> 4 [label=\"output\"]\n 5[label=\"Shovill\"]\n 3 -> 5 [label=\"out1\"]\n 3 -> 5 [label=\"out2\"]\n kd4ae2fa690f74b22a03828d53396d49d[color=lightseagreen,label=\"Output\\nshovill_log\"]\n 5 -> kd4ae2fa690f74b22a03828d53396d49d\n 6[label=\"Quast\"]\n 5 -> 6 [label=\"contigs\"]\n ke153c7c430784516bc7a8824d62adee5[color=lightseagreen,label=\"Output\\nquast_output\"]\n 6 -> ke153c7c430784516bc7a8824d62adee5\n 7[label=\"Bandage Image\"]\n 5 -> 7 [label=\"contigs_graph\"]\n 8[label=\"Bandage Info\"]\n 5 -> 8 [label=\"contigs_graph\"]\n k3d516f90bc474007a50e8974dfa5d7df[color=lightseagreen,label=\"Output\\nbandage_info_output\"]\n 8 -> k3d516f90bc474007a50e8974dfa5d7df\n}",
"history": [
{
"hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
@@ -35609,8 +27376,8 @@
}
],
"license": "MIT",
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- "modified": "2024-12-09 08:53:32 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 662858b7-e6f1-4380-96f0-40c0eec02a38[\"Output\\nfastp_json\"];\n 3 --> 662858b7-e6f1-4380-96f0-40c0eec02a38;\n style 662858b7-e6f1-4380-96f0-40c0eec02a38 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC\"];\n 1 -->|output| 4;\n 5[\"Shovill\"];\n 3 -->|out1| 5;\n 3 -->|out2| 5;\n d4ae2fa6-90f7-4b22-a038-28d53396d49d[\"Output\\nshovill_log\"];\n 5 --> d4ae2fa6-90f7-4b22-a038-28d53396d49d;\n style d4ae2fa6-90f7-4b22-a038-28d53396d49d stroke:#2c3143,stroke-width:4px;\n 6[\"Quast\"];\n 5 -->|contigs| 6;\n e153c7c4-3078-4516-bc7a-8824d62adee5[\"Output\\nquast_output\"];\n 6 --> e153c7c4-3078-4516-bc7a-8824d62adee5;\n style e153c7c4-3078-4516-bc7a-8824d62adee5 stroke:#2c3143,stroke-width:4px;\n 7[\"Bandage Image\"];\n 5 -->|contigs_graph| 7;\n 8[\"Bandage Info\"];\n 5 -->|contigs_graph| 8;\n 3d516f90-bc47-4007-a50e-8974dfa5d7df[\"Output\\nbandage_info_output\"];\n 8 --> 3d516f90-bc47-4007-a50e-8974dfa5d7df;\n style 3d516f90-bc47-4007-a50e-8974dfa5d7df stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Genome Assembly of MRSA using Illumina MiSeq Data",
"outputs": [
{
@@ -35670,7 +27437,7 @@
{
"label": "fastp_json",
"output_name": "report_json",
- "uuid": "cb42cdd8-1c0b-48af-9c03-1baf41b049e0"
+ "uuid": "662858b7-e6f1-4380-96f0-40c0eec02a38"
}
]
},
@@ -35727,7 +27494,7 @@
{
"label": "shovill_log",
"output_name": "shovill_std_log",
- "uuid": "7179e5b2-71ec-45f1-ab07-7e41a6e48b73"
+ "uuid": "d4ae2fa6-90f7-4b22-a038-28d53396d49d"
}
]
},
@@ -35772,7 +27539,7 @@
{
"label": "quast_output",
"output_name": "report_html",
- "uuid": "cd6831ed-850e-4bb7-bf84-8dce374fc1d1"
+ "uuid": "e153c7c4-3078-4516-bc7a-8824d62adee5"
}
]
},
@@ -35817,7 +27584,7 @@
{
"label": "bandage_info_output",
"output_name": "outfile",
- "uuid": "21eae0ec-9064-4568-ad13-d0bab6d47c26"
+ "uuid": "3d516f90-bc47-4007-a50e-8974dfa5d7df"
}
]
}
@@ -35898,22 +27665,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: busco\n owner: iuc\n revisions: 41030a6c03b7\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n owner: iuc\n revisions: b768cc4cca40\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n owner: iuc\n revisions: f8113c25bc6b\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n owner: iuc\n revisions: 29dabd8db6f2\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n owner: iuc\n revisions: 3061c8b029e5\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json",
- "contributions": {
- "authorship": [
- "abretaud",
- "alexcorm",
- "r1corre",
- "lleroi",
- "stephanierobin"
- ],
- "reviewing": [
- "gallardoalba",
- "alexcorm",
- "abretaud",
- "shiltemann",
- "hexylena"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -35978,133 +27729,22 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
"twitter": "robinstphanie1",
"url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
- {
- "email": "alexandre.cormier@ifremer.fr",
- "id": "alexcorm",
- "joined": "2021-11",
- "name": "Alexandre Cormier",
- "orcid": "0000-0002-7775-8413",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
- "twitter": "allanssx",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/assembly/tutorials/assembly-quality-control",
"edam_operation": [
"Visualisation",
"Genome assembly",
- "De-novo assembly",
- "k-mer counting",
"Sequence assembly validation",
- "Phasing",
"Transcriptome assembly",
- "Scaffolding"
+ "Scaffolding",
+ "Phasing",
+ "k-mer counting",
+ "De-novo assembly"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"feedback_mean_note": null,
@@ -36138,17 +27778,17 @@
"objectives": [
"Assess assembly quality"
],
- "pageviews": 3223261,
+ "pageviews": 3246279,
"pub_date": "2022-08-26",
"questions": [
"Is my genome assembly ready for annotation and/or scaffolding?"
],
"short_id": "T00028",
"short_tools": [
+ "meryl",
+ "quast",
"merqury",
"chromeister",
- "quast",
- "meryl",
"busco"
],
"slides": true,
@@ -36160,11 +27800,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -36201,6 +27836,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -36256,10 +27895,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -36306,11 +27941,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -36355,6 +27985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -36387,10 +28021,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -36413,10 +28047,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -36464,11 +28094,6 @@
"state": "exact",
"version": "5.3.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.3.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -36514,6 +28139,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -36567,10 +28196,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -36603,8 +28228,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.5.a",
- "1.3.c"
+ "1.3.c",
+ "1.5.a"
]
},
{
@@ -36617,11 +28242,6 @@
"state": "exact",
"version": "1.5.a+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.5.a+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -36665,6 +28285,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -36717,10 +28341,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -36763,11 +28383,6 @@
"state": "exact",
"version": "1.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -36812,6 +28427,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -36844,8 +28463,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -36868,10 +28487,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -36914,11 +28529,6 @@
"state": "exact",
"version": "1.3+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy6"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -36963,6 +28573,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -36987,8 +28601,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
- "5.2.0+galaxy1"
+ "5.2.0+galaxy1",
+ "5.0.2+galaxy0"
]
},
{
@@ -37020,10 +28634,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -37062,23 +28672,23 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
"5.2.0+galaxy1",
+ "5.0.2+galaxy0",
"5.0.2+galaxy1",
"5.0.2+galaxy4",
- "5.0.2",
"4.1",
+ "5.0.2",
+ "5.0.2+galaxy2",
"5.0.2+galaxy5",
- "5.0.2+galaxy3",
- "5.0.2+galaxy2"
+ "5.0.2+galaxy3"
]
},
{
@@ -37086,11 +28696,6 @@
"state": "exact",
"version": "5.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -37149,7 +28754,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 277,
- "visitors": 1336799,
+ "visitors": 1346884,
"workflows": [
{
"creators": [
@@ -37304,7 +28909,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGCA_000146045.2_genomic.fna\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.flye.30x.fa\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.hifiasm.30x.fa\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSRR13577847_subreads.30x.fastq.gz\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Busco\"];\n 0 -->|output| 4;\n 5[\"Busco\"];\n 1 -->|output| 5;\n 6[\"Quast\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 2 -->|output| 6;\n 7[\"Busco\"];\n 2 -->|output| 7;\n 8[\"Chromeister\"];\n 0 -->|output| 8;\n 2 -->|output| 8;\n 9[\"Meryl\"];\n 3 -->|output| 9;\n 10[\"Merqury\"];\n 0 -->|output| 10;\n 9 -->|read_db| 10;\n 11[\"Merqury\"];\n 1 -->|output| 11;\n 9 -->|read_db| 11;\n 12[\"Merqury\"];\n 2 -->|output| 12;\n 9 -->|read_db| 12;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Genome Assembly Quality Control",
"outputs": [],
"parent_id": "assembly/assembly-quality-control",
@@ -37561,23 +29166,23 @@
],
"edam_operation": [
"Visualisation",
- "Data handling",
- "Variant calling",
- "Sequencing quality control",
- "Read pre-processing",
- "Sequence alignment analysis",
+ "Sequence trimming",
+ "Genome assembly",
"Sequence assembly validation",
- "Sequence file editing",
+ "Sequence assembly visualisation",
"Statistical calculation",
- "Genome assembly",
+ "Sequencing quality control",
"Formatting",
- "Primer removal",
"Sequence composition calculation",
- "Sequence assembly visualisation",
- "Read mapping",
- "Sequence trimming",
+ "Variant calling",
+ "Sequence file editing",
"Sequence contamination filtering",
- "Local alignment"
+ "Primer removal",
+ "Data handling",
+ "Local alignment",
+ "Sequence alignment analysis",
+ "Read mapping",
+ "Read pre-processing"
],
"edam_topic": [
"Metagenomics",
@@ -37605,7 +29210,7 @@
"layout": "tutorial_hands_on",
"level": "Introductory",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Describe what an assembly is",
"Describe what de-replication is",
@@ -37617,8 +29222,8 @@
"Apply appropriate tools for analyzing the quality of metagenomic assembly",
"Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
],
- "pageviews": 2,
- "pub_date": "2024-12-09",
+ "pageviews": 13,
+ "pub_date": "2024-12-13",
"questions": [
"Why metagenomic data should be assembled?",
"What is the difference between co-assembly and individual assembly?",
@@ -37648,24 +29253,24 @@
],
"short_id": "T00035",
"short_tools": [
- "fastqc",
- "collection_column_join",
- "bg_uniq",
- "tp_cat",
- "bowtie2",
+ "bandage_info",
+ "bandage_image",
"megahit",
- "cutadapt",
- "random_lines1",
"megahit_contig2fastg",
+ "metaspades",
"ngsutils_bam_filter",
- "filter_tabular",
- "bandage_info",
"quast",
+ "tp_cat",
+ "fastqc",
+ "bg_uniq",
+ "cutadapt",
+ "filter_tabular",
+ "random_lines1",
"seqtk_subseq",
- "metaspades",
- "bamtools",
"coverm_contig",
- "bandage_image"
+ "collection_column_join",
+ "bamtools",
+ "bowtie2"
],
"slides": false,
"slides_recordings": false,
@@ -37707,6 +29312,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -37762,10 +29371,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -37812,11 +29417,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -37861,6 +29461,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -37913,10 +29517,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -37957,10 +29557,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -38003,6 +29599,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38057,10 +29657,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -38109,11 +29705,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -38159,6 +29750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38212,10 +29807,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -38259,11 +29850,6 @@
"state": "exact",
"version": "0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -38306,6 +29892,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38361,10 +29951,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -38400,9 +29986,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.0.1",
+ "2.4.0.0",
"2.4.0",
- "2.4.0.0"
+ "0.0.1"
]
},
{
@@ -38417,11 +30003,6 @@
"state": "exact",
"version": "2.5.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -38469,6 +30050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38503,9 +30088,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -38529,10 +30114,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -38568,13 +30149,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -38583,12 +30164,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -38597,11 +30178,6 @@
"state": "exact",
"version": "2.4.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.5+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -38647,6 +30223,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38671,9 +30251,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -38685,9 +30265,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -38711,10 +30291,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -38750,13 +30326,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -38770,17 +30346,12 @@
"state": "exact",
"version": "2.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.4.5+galaxy1",
"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -38827,6 +30398,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -38884,10 +30459,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -38913,8 +30484,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -38938,12 +30509,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -38953,9 +30524,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -38966,11 +30537,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -39016,6 +30582,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39077,10 +30647,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -39135,11 +30701,6 @@
"state": "exact",
"version": "0.8.1+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -39189,6 +30750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39250,10 +30815,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -39304,11 +30865,6 @@
"state": "exact",
"version": "0.8.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -39354,6 +30910,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39407,10 +30967,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -39455,11 +31011,6 @@
"state": "exact",
"version": "0.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -39505,6 +31056,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39558,10 +31113,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -39607,14 +31158,6 @@
"state": "exact",
"version": "0.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.7.0+galaxy0",
- "0.6.1+galaxy3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -39657,6 +31200,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39715,10 +31262,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -39768,10 +31311,6 @@
"state": "exact",
"version": "2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -39817,6 +31356,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -39876,10 +31419,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -39933,11 +31472,6 @@
"state": "exact",
"version": "1.2.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -39983,6 +31517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40036,10 +31574,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -40083,11 +31617,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -40133,6 +31662,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40188,10 +31721,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -40241,13 +31770,6 @@
"1.1.3+galaxy1"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.3+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -40299,6 +31821,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40351,10 +31877,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -40398,11 +31920,6 @@
"state": "exact",
"version": "0.5.9"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.9"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -40448,6 +31965,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40472,8 +31993,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
- "5.2.0+galaxy1"
+ "5.2.0+galaxy1",
+ "5.0.2+galaxy0"
]
},
{
@@ -40505,10 +32026,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -40547,23 +32064,23 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
"5.2.0+galaxy1",
+ "5.0.2+galaxy0",
"5.0.2+galaxy1",
"5.0.2+galaxy4",
- "5.0.2",
"4.1",
+ "5.0.2",
+ "5.0.2+galaxy2",
"5.0.2+galaxy5",
- "5.0.2+galaxy3",
- "5.0.2+galaxy2"
+ "5.0.2+galaxy3"
]
},
{
@@ -40571,11 +32088,6 @@
"state": "exact",
"version": "5.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -40621,6 +32133,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40675,10 +32191,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -40715,8 +32227,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -40729,11 +32241,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -40779,6 +32286,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40833,10 +32344,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -40883,11 +32390,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -40934,6 +32436,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -40970,8 +32476,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -40994,10 +32500,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -41040,8 +32542,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -41056,11 +32558,6 @@
"state": "exact",
"version": "4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -41108,6 +32605,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -41161,10 +32662,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -41214,11 +32711,6 @@
"state": "exact",
"version": "3.15.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.15.4+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -41293,8 +32785,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 0,
- "visitors": 2,
+ "visit_duration": 103,
+ "visitors": 11,
"workflows": [
{
"creators": [],
@@ -41343,7 +32835,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"metaSPAdes\"];\n 0 -->|output| 1;\n 833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n 1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n 10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n 1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n 1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n 1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n 2[\"MEGAHIT\"];\n 0 -->|output| 2;\n 3[\"Bowtie2\"];\n 0 -->|output| 3;\n 2 -->|output| 3;\n 4[\"megahit contig2fastg\"];\n 2 -->|output| 4;\n 5[\"Quast\"];\n 2 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Bandage Image\"];\n 4 -->|fastg| 6;\n 7[\"Bandage Info\"];\n 4 -->|fastg| 7;\n 8[\"Column join\"];\n 7 -->|outfile| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Metagenomics assembly tutorial workflow",
"outputs": [
{
@@ -41927,7 +33419,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Cutadapt\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"MEGAHIT\"];\n 2 -->|out1| 3;\n 2 -->|out2| 3;\n 4[\"Bowtie2\"];\n 2 -->|out1| 4;\n 2 -->|out2| 4;\n 3 -->|output| 4;\n 5[\"BAM filter\"];\n 4 -->|output| 5;\n 6[\"BAM filter\"];\n 4 -->|output| 6;\n 7[\"Convert, Merge, Randomize\"];\n 5 -->|outfile| 7;\n 8[\"Convert, Merge, Randomize\"];\n 6 -->|outfile| 8;\n 9[\"Select random lines\"];\n 7 -->|out_file1| 9;\n 10[\"Select random lines\"];\n 8 -->|out_file1| 10;\n 11[\"Filter Tabular\"];\n 9 -->|out_file1| 11;\n 12[\"Filter Tabular\"];\n 10 -->|out_file1| 12;\n 13[\"Unique\"];\n 11 -->|output| 13;\n 14[\"Unique\"];\n 12 -->|output| 14;\n 15[\"Concatenate datasets\"];\n 13 -->|outfile| 15;\n 14 -->|outfile| 15;\n 16[\"seqtk_subseq\"];\n 2 -->|out1| 16;\n 15 -->|out_file1| 16;\n 17[\"seqtk_subseq\"];\n 2 -->|out2| 17;\n 15 -->|out_file1| 17;\n 18[\"FastQC\"];\n 16 -->|default| 18;\n 19[\"FastQC\"];\n 17 -->|default| 19;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "workflow-generate-dataset-for-assembly-tutorial",
"outputs": [
{
@@ -42981,18 +34473,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n owner: bgruening\n revisions: 291923e6f276\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n owner: bgruening\n revisions: 78c533842eeb\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 5ec9f6bceaee\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: ddddce450736\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: ea8146ee148f\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n owner: iuc\n revisions: 0dbb995c7d35\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n revisions: c59d48774d03\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n owner: iuc\n revisions: 01210c4e9144\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n owner: iuc\n revisions: fc8804320156\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n owner: iuc\n revisions: 29dabd8db6f2\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n owner: iuc\n revisions: be1d967337e4\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n owner: iuc\n revisions: a02b8b3f5a0c\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n owner: iuc\n revisions: 72472698a2df\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
- "contributions": {
- "authorship": [
- "annasyme"
- ],
- "reviewing": [
- "shiltemann",
- "deeptivarshney",
- "hexylena",
- "annasyme",
- "gallardoalba"
- ]
- },
"contributors": [
{
"id": "annasyme",
@@ -43001,124 +34481,30 @@
"orcid": "0000-0002-9906-0673",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "deeptivarshney",
- "joined": "2022-12",
- "name": "Deepti Varshney",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "id": "annasyme",
- "joined": "2017-09",
- "name": "Anna Syme",
- "orcid": "0000-0002-9906-0673",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
}
],
"dir": "topics/assembly/tutorials/largegenome",
"edam_operation": [
- "Visualisation",
- "Variant calling",
+ "Validation",
+ "Sequence assembly visualisation",
+ "Cross-assembly",
+ "Scaffolding",
"Sequencing quality control",
+ "Sequence composition calculation",
+ "Sequence contamination filtering",
+ "Sequence assembly",
"De-novo assembly",
- "Box-Whisker plot plotting",
- "Validation",
+ "Visualisation",
"Pairwise sequence alignment",
+ "Genome assembly",
+ "Base-calling",
"Sequence assembly validation",
"Transcriptome assembly",
- "Sequence assembly",
- "Scatter plot plotting",
"Statistical calculation",
- "Genome assembly",
- "Base-calling",
+ "Variant calling",
+ "Scatter plot plotting",
"Mapping assembly",
- "Sequence composition calculation",
- "Sequence assembly visualisation",
- "Cross-assembly",
- "Scaffolding",
- "Sequence contamination filtering"
+ "Box-Whisker plot plotting"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -43149,7 +34535,7 @@
"Polish the assembly",
"Assess the quality of the assembly"
],
- "pageviews": 5990,
+ "pageviews": 6048,
"pub_date": "2023-03-06",
"questions": [
"How can we assemble a large plant or animal genome?"
@@ -43170,21 +34556,21 @@
],
"short_id": "T00331",
"short_tools": [
- "fastqc",
- "fasta-stats",
- "nanoplot",
- "multiqc",
- "flye",
- "racon",
- "medaka_consensus_pipeline",
+ "genomescope",
"minimap2",
+ "bandage_image",
"fastp",
- "quast",
"meryl",
+ "quast",
"barchart_gnuplot",
- "bandage_image",
- "busco",
- "genomescope"
+ "fastqc",
+ "racon",
+ "fasta-stats",
+ "medaka_consensus_pipeline",
+ "multiqc",
+ "nanoplot",
+ "flye",
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -43231,6 +34617,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -43286,10 +34676,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -43336,11 +34722,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -43385,6 +34766,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -43437,10 +34822,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -43481,10 +34862,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -43527,6 +34904,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -43563,10 +34944,11 @@
"state": "inexact",
"versions": [
"2.9.4+galaxy0",
- "2.6",
"2.9.1+galaxy0",
"2.8.2+galaxy0",
- "2.9+galaxy0"
+ "2.9+galaxy0",
+ "2.6",
+ "2.9.5+galaxy1"
]
},
{
@@ -43589,10 +34971,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -43633,10 +35011,10 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.6",
"2.9.1+galaxy0",
"2.8.2+galaxy0",
"2.9+galaxy0",
+ "2.6",
"2.3.7",
"2.3.5",
"2.8.3+galaxy0"
@@ -43647,11 +35025,6 @@
"state": "exact",
"version": "2.9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -43697,6 +35070,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -43750,10 +35127,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -43786,8 +35159,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.1",
- "1.3.1.1"
+ "1.3.1.1",
+ "1.3.1"
]
},
{
@@ -43800,11 +35173,6 @@
"state": "exact",
"version": "1.5.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.5.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -43855,6 +35223,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -43880,8 +35252,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -43918,10 +35290,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -43945,8 +35313,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -43966,12 +35334,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -43984,11 +35352,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -44037,6 +35400,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -44094,10 +35461,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -44147,11 +35510,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -44197,6 +35555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -44229,10 +35591,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -44255,10 +35617,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -44306,23 +35664,18 @@
"state": "exact",
"version": "5.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -44365,6 +35718,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -44422,10 +35779,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -44471,11 +35824,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -44521,6 +35869,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -44585,10 +35937,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -44624,11 +35972,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -44643,11 +35991,6 @@
"state": "exact",
"version": "0.23.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -44664,9 +36007,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -44707,6 +36050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -44760,10 +36107,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -44806,11 +36149,6 @@
"state": "exact",
"version": "2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -44857,164 +36195,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
- "1.0.3+galaxy2",
- "1.3.2+galaxy0",
- "1.0.3+galaxy1"
- ]
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "1.0.3+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "1.0.3+galaxy2",
- "1.3.2+galaxy0",
- "1.4.4+galaxy1",
- "1.4.4+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "1.7.2+galaxy1"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -45049,8 +36230,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.0.3+galaxy1",
+ "1.0.3+galaxy2",
+ "1.3.2+galaxy0"
]
},
{
@@ -45073,10 +36255,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -45107,20 +36285,170 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "1.0.3+galaxy2"
+ ]
},
{
"server": "https://usegalaxy.cz/",
"state": "exact",
- "version": "1.3+galaxy6"
+ "version": "1.7.2+galaxy1"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "1.7.2+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.0.3+galaxy2",
+ "1.3.2+galaxy0",
+ "1.4.4+galaxy1",
+ "1.4.4+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.7.2+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.7.2+galaxy1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.7.2+galaxy1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "1.2+galaxy1",
+ "1.3+galaxy1"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
"version": "1.3+galaxy6"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.3+galaxy6"
},
@@ -45168,6 +36496,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -45192,8 +36524,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
+ "2.28+galaxy0",
+ "2.24+galaxy0"
]
},
{
@@ -45205,8 +36537,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -45229,10 +36561,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -45269,12 +36597,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -45287,11 +36615,6 @@
"state": "exact",
"version": "2.26+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.26+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -45340,6 +36663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -45394,10 +36721,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -45446,11 +36769,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -45461,8 +36779,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -45505,6 +36823,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -45566,10 +36888,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -45623,11 +36941,6 @@
"state": "exact",
"version": "1.42.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.42.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -45677,6 +36990,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -45731,10 +37048,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -45771,8 +37084,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -45785,11 +37098,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -45860,7 +37168,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 129,
- "visitors": 4581,
+ "visitors": 4628,
"workflows": [
{
"creators": [
@@ -46035,7 +37343,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 4;\n 1 -->|output| 4;\n 2 -->|output| 4;\n 5[\"Medaka polish\"];\n 4 -->|Assembly polished by long reads using Racon| 5;\n 1 -->|output| 5;\n e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n 5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n 6[\"Fasta statistics after Racon long read polish\"];\n 4 -->|Assembly polished by long reads using Racon| 6;\n 7[\"Fasta statistics after Medaka polish\"];\n 5 -->|out_consensus| 7;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 5 -->|out_consensus| 8;\n 3 -->|output| 8;\n 9[\"Fasta statistics after Racon short read polish\"];\n 8 -->|Assembly polished by short reads using Racon| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assembly polishing - upgraded",
"outputs": [
{
@@ -46873,7 +38181,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Flye: assembly\"];\n 0 -->|output| 1;\n 3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n 1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n 1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n 48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n 1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n 8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n 1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n 2[\"Fasta statistics\"];\n 1 -->|consensus| 2;\n 3[\"Quast genome report\"];\n 1 -->|consensus| 3;\n 17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s): HTML report\"];\n 3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n 4[\"Bandage image: Flye assembly\"];\n 1 -->|assembly_gfa| 4;\n e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n 4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n 5[\"Bar chart: show contig sizes\"];\n 1 -->|assembly_info| 5;\n 6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n 5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assembly with Flye - upgraded",
"outputs": [
{
@@ -47218,7 +38526,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Busco: assess assembly\"];\n 0 -->|output| 2;\n 219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n 2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n 3[\"Quast: assess assembly\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s): HTML report\"];\n 3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assess genome quality - upgraded",
"outputs": [
{
@@ -47549,7 +38857,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n style 5 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 5;\n 6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n style 6 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 6;\n 2 -->|output| 6;\n 0 -->|output| 6;\n 7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n style 7 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 7;\n 2 -->|output| 7;\n 0 -->|output| 7;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 7 -->|fastp filtered long reads| 8;\n 9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n style 9 fill:#edd,stroke:#900,stroke-width:4px;\n 8 -->|Flye assembly on input datasets consensus| 9;\n 7 -->|fastp filtered R1 reads| 9;\n 7 -->|fastp filtered long reads| 9;\n 3 -->|output| 9;\n 10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n style 10 fill:#edd,stroke:#900,stroke-width:4px;\n 9 -->|Assembly polished by long reads using Medaka| 10;\n 4 -->|output| 10;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Combined workflows for large genome assembly - upgraded ",
"outputs": [
{
@@ -49085,7 +40393,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Nanoplot: long reads\"];\n 0 -->|output| 3;\n 73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n 3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC on R1\"];\n 1 -->|output| 4;\n 5[\"FastQC on R2\"];\n 2 -->|output| 5;\n 6[\"MultiQC: combine fastQC reports\"];\n 4 -->|text_file| 6;\n 5 -->|text_file| 6;\n 8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n 6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Data QC - upgraded",
"outputs": [
{
@@ -49358,7 +40666,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Minimap2 round 1: map reads to assembly\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Racon round 1: polish assembly\"];\n 0 -->|output| 3;\n 2 -->|alignment_output| 3;\n 1 -->|output| 3;\n 4[\"Minimap2 round 2: map reads to assembly\"];\n 1 -->|output| 4;\n 3 -->|consensus| 4;\n 5[\"Racon round 2: polish assembly\"];\n 3 -->|consensus| 5;\n 4 -->|alignment_output| 5;\n 1 -->|output| 5;\n 594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n 5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
"outputs": [
{
@@ -49593,7 +40901,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"Minimap2: map long reads to assembly\"];\n 2 -->|output| 3;\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Racon: polish 1\"];\n 0 -->|output| 4;\n 3 -->|alignment_output| 4;\n 1 -->|output| 4;\n 5[\"Minimap2: map long reads to polished assembly 1\"];\n 2 -->|output| 5;\n 1 -->|output| 5;\n 4 -->|consensus| 5;\n 6[\"Racon: polish 2\"];\n 4 -->|consensus| 6;\n 5 -->|alignment_output| 6;\n 1 -->|output| 6;\n 7[\"Minimap2: map long reads to polished assembly 2\"];\n 2 -->|output| 7;\n 1 -->|output| 7;\n 6 -->|consensus| 7;\n 8[\"Racon: polish 3\"];\n 6 -->|consensus| 8;\n 7 -->|alignment_output| 8;\n 1 -->|output| 8;\n 9[\"Minimap2: map long reads to polished assembly 3\"];\n 2 -->|output| 9;\n 1 -->|output| 9;\n 8 -->|consensus| 9;\n 10[\"Racon: polish 4\"];\n 8 -->|consensus| 10;\n 9 -->|alignment_output| 10;\n 1 -->|output| 10;\n bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n 10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Racon polish with long reads, x4 - upgraded",
"outputs": [
{
@@ -49855,7 +41163,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"fastp on short reads\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n 3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n 0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n 3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n 10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n 3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n 639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n 3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n 4[\"fastp on long reads\"];\n 2 -->|output| 4;\n 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n 4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n 4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n 69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n 4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Trim and filter reads - fastp - upgraded ",
"outputs": [
{
@@ -50182,7 +41490,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Meryl - count kmers\"];\n 0 -->|output| 1;\n 899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n 1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n 2[\"Meryl - generate histogram\"];\n 1 -->|read_db| 2;\n 3[\"Genomescope\"];\n 2 -->|read_db_hist| 3;\n efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n 3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n 701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n 3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n 85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n 3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n 3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "kmer counting - meryl - upgraded",
"outputs": [
{
@@ -50441,15 +41749,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: mitohifi\n owner: bgruening\n revisions: 99ddbf037d98\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compress_file\n owner: iuc\n revisions: '09ea79f9f260'\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mitochondrion-assembly/tutorial.json",
- "contributions": {
- "authorship": [
- "delphine-l"
- ],
- "reviewing": [
- "teresa-m",
- "bgruening"
- ]
- },
"contributors": [
{
"email": "delphine.lariviere@galaxy.org",
@@ -50459,48 +41758,6 @@
"orcid": "0000-0001-6421-3484",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/assembly/tutorials/mitochondrion-assembly",
@@ -50531,7 +41788,7 @@
"Generate Mitochondrial assembly",
"Understand the outputs of MitoHifi"
],
- "pageviews": 258,
+ "pageviews": 271,
"pub_date": "2024-09-03",
"questions": [
"How to assemble the mitochondrial genome from PacBio Hifi Reads"
@@ -50605,6 +41862,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -50660,10 +41921,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -50710,11 +41967,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -50759,6 +42011,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -50812,10 +42068,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -50858,10 +42110,6 @@
"state": "exact",
"version": "3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -50906,6 +42154,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -50958,10 +42210,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -51004,10 +42252,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -51057,8 +42301,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 122,
- "visitors": 209,
+ "visit_duration": 113,
+ "visitors": 219,
"workflows": [
{
"creators": [
@@ -51193,7 +42437,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nCollection of Pacbio Data\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nSpecies name latin name\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nEmail adress\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"MitoHiFi\"];\n 2 -->|output| 3;\n 1 -->|output| 3;\n 4[\"MitoHiFi\"];\n 0 -->|output| 4;\n 3 -->|fasta_reference| 4;\n 3 -->|genbank_reference| 4;\n 31807e4b-e616-4742-92e0-934e6c3c09ae[\"Output\\ncontigs_stats\"];\n 4 --> 31807e4b-e616-4742-92e0-934e6c3c09ae;\n style 31807e4b-e616-4742-92e0-934e6c3c09ae stroke:#2c3143,stroke-width:4px;\n 8393c665-a328-4698-93e5-198c6fea52dd[\"Output\\nmitogenome_coverage\"];\n 4 --> 8393c665-a328-4698-93e5-198c6fea52dd;\n style 8393c665-a328-4698-93e5-198c6fea52dd stroke:#2c3143,stroke-width:4px;\n 85061673-df5e-480d-920a-a11c72bf8f56[\"Output\\nmitogenome_annotation\"];\n 4 --> 85061673-df5e-480d-920a-a11c72bf8f56;\n style 85061673-df5e-480d-920a-a11c72bf8f56 stroke:#2c3143,stroke-width:4px;\n fe4d1d3d-9caa-45f6-944e-c4b101105dd1[\"Output\\nmitogenome_genbank\"];\n 4 --> fe4d1d3d-9caa-45f6-944e-c4b101105dd1;\n style fe4d1d3d-9caa-45f6-944e-c4b101105dd1 stroke:#2c3143,stroke-width:4px;\n 5[\"Compress files\"];\n 4 -->|mitogenome_fasta| 5;\n 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed[\"Output\\noutput_file\"];\n 5 --> 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed;\n style 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Mitogenome-Assembly-VGP0",
"outputs": [
{
@@ -51890,23 +43134,23 @@
"topic_4013"
],
"edam_operation": [
- "Scatter plot plotting",
"Visualisation",
+ "Filtering",
+ "Genome assembly",
+ "Sequence assembly validation",
+ "Sequence assembly visualisation",
+ "Cross-assembly",
"Statistical calculation",
"Sequencing quality control",
- "Genome assembly",
+ "Sequence composition calculation",
+ "Sequence contamination filtering",
"Sequencing error detection",
- "De-novo assembly",
+ "Read mapping",
"Mapping assembly",
- "Box-Whisker plot plotting",
- "Filtering",
- "Sequence assembly validation",
"Sequence alignment",
- "Sequence composition calculation",
- "Sequence assembly visualisation",
- "Read mapping",
- "Cross-assembly",
- "Sequence contamination filtering"
+ "Scatter plot plotting",
+ "De-novo assembly",
+ "Box-Whisker plot plotting"
],
"edam_topic": [
"Sequence assembly",
@@ -51962,7 +43206,7 @@
"Run tools to assess the quality of an assembly",
"Understand the outputs of tools to assess the quality of an assembly"
],
- "pageviews": 11749,
+ "pageviews": 11866,
"pub_date": "2021-03-24",
"questions": [
"How to check the quality of the MinION data (together with Illumina data)?",
@@ -51971,18 +43215,18 @@
],
"short_id": "T00037",
"short_tools": [
- "fastqc",
"polypolish",
- "nanoplot",
- "CONVERTER_bz2_to_uncompressed",
+ "bandage_image",
+ "fastp",
+ "quast",
+ "fastqc",
"filtlong",
+ "nanoplot",
"flye",
- "quast",
"upload1",
- "fastp",
+ "bwa_mem2",
"porechop",
- "bandage_image",
- "bwa_mem2"
+ "CONVERTER_bz2_to_uncompressed"
],
"slides": false,
"slides_recordings": false,
@@ -52024,6 +43268,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -52079,10 +43327,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -52129,11 +43373,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -52178,6 +43417,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -52230,10 +43473,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -52274,10 +43513,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -52320,6 +43555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -52376,10 +43615,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -52426,17 +43661,12 @@
"state": "exact",
"version": "2.9.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.6",
"2.9+galaxy0",
+ "2.6",
"2.8.3+galaxy0",
"2.9.3+galaxy0",
"2.6+galaxy0"
@@ -52482,6 +43712,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -52507,8 +43741,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -52545,10 +43779,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -52572,8 +43802,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -52593,12 +43823,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -52611,11 +43841,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -52664,6 +43889,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -52722,14 +43951,163 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
"state": "missing"
},
{
- "server": "https://mississippi.sorbonne-universite.fr",
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.8.1+galaxy0+galaxy0",
+ "0.8.1+galaxy1",
+ "0.8.1+galaxy0",
+ "0.8.1+galaxy2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "server": "https://usegalaxy.org",
"state": "exact",
"version": "2022.09+galaxy4"
},
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "2022.09+galaxy4"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "2.2.1+galaxy0"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "2.2.1+galaxy1"
+ },
{
"server": "https://neo.engr.uconn.edu/",
"state": "missing"
@@ -52756,53 +44134,41 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "0.8.1+galaxy0+galaxy0",
- "0.8.1+galaxy1",
- "0.8.1+galaxy0",
- "0.8.1+galaxy2"
- ]
+ "state": "missing"
},
{
"server": "https://usegalaxy.cz/",
"state": "exact",
- "version": "2022.09+galaxy4"
+ "version": "2.2.1+galaxy1"
},
{
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- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
+ "version": "2.2.1+galaxy1"
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{
"server": "https://usegalaxy.no/",
- "state": "exact",
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+ "state": "missing"
},
{
"server": "https://usegalaxy.org",
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+ "version": "2.2.1+galaxy1"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
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+ "version": "2.2.1+galaxy1"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
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},
{
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@@ -52824,6 +44190,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -52846,18 +44216,18 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
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+ "state": "exact",
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{
"server": "https://galaxy.pasteur.fr/",
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+ "state": "exact",
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{
"server": "https://galaxytrakr.org/",
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- "versions": [
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- ]
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -52879,14 +44249,12 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "2.2.1+galaxy1"
+ "state": "inexact",
+ "versions": [
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+ ]
},
{
"server": "https://neo.engr.uconn.edu/",
@@ -52914,46 +44282,52 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
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+ "0.19.5+galaxy1",
+ "0.19.3.2",
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
+ ]
},
{
"server": "https://usegalaxy.cz/",
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+ "version": "0.23.2+galaxy0"
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{
"server": "https://usegalaxy.eu",
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+ "version": "0.23.2+galaxy0"
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{
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+ "state": "exact",
+ "version": "0.23.2+galaxy0"
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{
"server": "https://usegalaxy.org",
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{
"server": "https://usegalaxy.org.au",
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- "version": "2.2.1+galaxy1"
+ "version": "0.23.2+galaxy0"
},
{
"server": "https://viralvariant.anses.fr/",
- "state": "missing"
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
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{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
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@@ -52975,6 +44349,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -52997,18 +44375,22 @@
},
{
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+ "state": "missing"
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
+ "state": "inexact",
+ "versions": [
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+ ]
},
{
"server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
+ "state": "inexact",
+ "versions": [
+ "0.2.1+galaxy0",
+ "0.2.0+galaxy1"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -53030,16 +44412,9 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
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- ]
+ "state": "missing"
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{
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@@ -53067,57 +44442,45 @@
},
{
"server": "https://usegalaxy.be/",
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- "0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
- "0.19.3.2",
- "0.19.5"
- ]
+ "state": "exact",
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{
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- "state": "exact",
- "version": "0.23.2+galaxy0"
+ "state": "inexact",
+ "versions": [
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+ ]
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{
"server": "https://usegalaxy.eu",
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- },
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+ "version": "0.2.0"
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{
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+ "version": "0.2.0"
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{
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+ "version": "0.2.0"
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{
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+ "version": "0.2.0"
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{
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+ "state": "missing"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
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@@ -53139,6 +44502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -53165,18 +44532,13 @@
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{
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+ "state": "exact",
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- ]
+ "state": "exact",
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{
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@@ -53198,10 +44560,6 @@
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@@ -53232,52 +44590,45 @@
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+ "0.2.0"
]
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{
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+ "server": "https://usegalaxy.cz/",
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{
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
+ "server": "https://usegalaxy.eu",
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{
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+ "version": "0.2.1+galaxy0"
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{
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+ "version": "0.2.1+galaxy0"
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{
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}
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{
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"servers": [
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@@ -53299,6 +44650,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
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@@ -53321,17 +44676,24 @@
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{
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+ "state": "inexact",
+ "versions": [
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+ ]
},
{
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+ "state": "inexact",
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+ ]
},
{
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+ "state": "inexact",
+ "versions": [
+ "1.28.2+galaxy1"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -53353,13 +44715,12 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- },
{
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+ "state": "inexact",
+ "versions": [
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+ ]
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{
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@@ -53389,48 +44750,50 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
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+ "1.28.2+galaxy1",
+ "1.13.0",
+ "1.25.0+galaxy0",
+ "1.25.0+galaxy1"
]
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{
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{
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+ "state": "inexact",
+ "versions": [
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+ "1.25.0+galaxy1",
+ "1.36.2+galaxy1"
+ ]
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{
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+ "version": "1.41.0+galaxy0"
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{
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"state": "missing"
}
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},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
"servers": [
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@@ -53452,6 +44815,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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@@ -53474,24 +44841,16 @@
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- "state": "inexact",
- "versions": [
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- ]
+ "state": "missing"
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{
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- "state": "inexact",
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- ]
+ "state": "missing"
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{
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- "versions": [
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- ]
+ "state": "exact",
+ "version": "0.5.0+galaxy2"
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{
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@@ -53513,172 +44872,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -53771,6 +44959,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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@@ -53928,6 +45112,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -53982,10 +45170,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -54022,8 +45206,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -54036,11 +45220,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -54086,6 +45265,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -54138,10 +45321,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -54182,10 +45361,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -54251,7 +45426,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 204,
- "visitors": 7694,
+ "visitors": 7768,
"workflows": [
{
"creators": [
@@ -54368,7 +45543,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Convert compressed file to uncompressed.\"];\n 0 -->|output| 3;\n 4[\"FastQC\"];\n 0 -->|output| 4;\n 5[\"fastp\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 6[\"NanoPlot\"];\n 3 -->|output1| 6;\n a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n 6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n 7[\"filtlong\"];\n 5 -->|out1| 7;\n 5 -->|out2| 7;\n 0 -->|output| 7;\n 8[\"Flye\"];\n 7 -->|outfile| 8;\n f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n 8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n 9[\"NanoPlot\"];\n 7 -->|outfile| 9;\n 89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n 9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n 10[\"Bandage Image\"];\n 8 -->|assembly_gfa| 10;\n 11[\"BWA-MEM2\"];\n 5 -->|out2| 11;\n 8 -->|consensus| 11;\n 12[\"Quast\"];\n 8 -->|consensus| 12;\n dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n 12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n 13[\"BWA-MEM2\"];\n 5 -->|out1| 13;\n 8 -->|consensus| 13;\n 14[\"Polypolish\"];\n 8 -->|consensus| 14;\n 13 -->|bam_output| 14;\n 11 -->|bam_output| 14;\n 15[\"Quast\"];\n 14 -->|polished_fasta| 15;\n 8 -->|consensus| 15;\n 4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n 15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
"outputs": [
{
@@ -54796,18 +45971,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n owner: devteam\n revisions: 749c918495f7\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n owner: devteam\n revisions: 8cacfcf96a52\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n owner: devteam\n revisions: 145f6d74ff5e\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: b2860df42e16\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: 94fe43e75ddc\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n revisions: 1d8fe9bc4cb0\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n owner: iuc\n revisions: 53c0b7a1a0c3\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: b2f1f75d49c4\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n owner: iuc\n revisions: 645159bcee2d\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n owner: iuc\n revisions: a8d69aee190e\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n owner: iuc\n revisions: b01db2684fa5\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n owner: iuc\n revisions: 3da72230c066\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n owner: iuc\n revisions: aad3885b3216\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n owner: iuc\n revisions: 9e3e80cc4ad4\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 830961c48e42\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
- "contributions": {
- "authorship": [
- "wm75"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "wm75",
- "bgruening",
- "slugger70"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -54825,143 +45988,22 @@
"orcid": "0000-0002-9464-6640",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "by-covid",
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "elixir_node": "au",
- "email": "simon.gladman@unimelb.edu.au",
- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
- "orcid": "0000-0002-6100-4385",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
}
],
"dir": "topics/assembly/tutorials/assembly-with-preprocessing",
"edam_operation": [
- "Scatter plot plotting",
- "Data handling",
- "Sequencing quality control",
- "Genome assembly",
- "Pairwise sequence alignment",
- "Box-Whisker plot plotting",
"Validation",
+ "Pairwise sequence alignment",
+ "Genome assembly",
+ "Read mapping",
+ "Sequence assembly visualisation",
+ "Sequencing quality control",
"Sequence file editing",
+ "Data handling",
+ "Sequence contamination filtering",
"Aggregation",
- "Sequence assembly visualisation",
- "Read mapping",
- "Sequence contamination filtering"
+ "Scatter plot plotting",
+ "Box-Whisker plot plotting"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -54976,7 +46018,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -54999,7 +46040,7 @@
"Detect and remove human reads",
"Assemble retained reads and explore the results"
],
- "pageviews": 6187138,
+ "pageviews": 6210145,
"pub_date": "2020-04-21",
"questions": [
"How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
@@ -55044,22 +46085,22 @@
],
"short_id": "T00029",
"short_tools": [
+ "bandage_info",
+ "collapse_dataset",
+ "minimap2",
+ "bandage_image",
+ "fastp",
+ "unicycler",
"fasta_filter_by_length",
- "samtools_view",
- "seqtk_sample",
- "bowtie2",
+ "multiqc",
+ "samtools_stats",
"nanoplot",
+ "samtools_view",
"samtools_fastx",
- "multiqc",
- "minimap2",
"fasterq_dump",
- "bandage_info",
- "unicycler",
- "fastp",
- "samtools_stats",
- "bandage_image",
"__ZIP_COLLECTION__",
- "collapse_dataset"
+ "bowtie2",
+ "seqtk_sample"
],
"slides": true,
"slides_recordings": false,
@@ -55092,11 +46133,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -55131,6 +46167,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -55186,10 +46226,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -55236,11 +46272,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -55285,6 +46316,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -55337,10 +46372,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -55381,10 +46412,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -55427,6 +46454,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -55451,9 +46482,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -55485,10 +46516,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -55530,12 +46557,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -55544,11 +46571,6 @@
"state": "exact",
"version": "2.3.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.3.4.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -55594,6 +46616,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -55646,10 +46672,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -55694,11 +46716,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -55744,6 +46761,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -55804,10 +46825,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -55856,11 +46873,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -55906,6 +46918,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -55930,8 +46946,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.8.1+galaxy0+galaxy0",
"0.8.1+galaxy4",
+ "0.8.1+galaxy0+galaxy0",
"2022.09+galaxy4"
]
},
@@ -55971,10 +46987,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -56024,11 +47036,6 @@
"state": "exact",
"version": "0.8.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -56074,6 +47081,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -56098,9 +47109,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.8.1+galaxy2",
+ "2022.09+galaxy2",
"0.8.1+galaxy0+galaxy0",
- "2022.09+galaxy2"
+ "0.8.1+galaxy2"
]
},
{
@@ -56133,16 +47144,12 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
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- "2022.09+galaxy2"
+ "2022.09+galaxy2",
+ "0.8.1+galaxy2"
]
},
{
@@ -56186,11 +47193,6 @@
"state": "exact",
"version": "0.8.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -56237,168 +47239,7 @@
"state": "missing"
},
{
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- "server": "http://cropgalaxy.excellenceinbreeding.org/",
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- {
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- {
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- {
- "server": "https://galaxy.mesocentre.uca.fr",
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- "server": "https://galaxy.pasteur.fr/",
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- ]
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- {
- "server": "https://galaxytrakr.org/",
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- "0.23.2+galaxy0"
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- "server": "http://hyperbrowser.uio.no/hb/",
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- {
- "server": "http://gigagalaxy.net/",
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- "server": "https://www.immportgalaxy.org/",
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- ]
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- "server": "https://neo.engr.uconn.edu/",
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- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
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- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
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- "server": "https://palfinder.ls.manchester.ac.uk/",
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- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
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- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
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- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "0.19.5+galaxy1"
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- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.19.5+galaxy1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.19.5+galaxy1"
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- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.19.5+galaxy1"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "0.19.5+galaxy1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "0.19.5+galaxy1"
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- {
- "server": "https://viralvariant.anses.fr/",
- "state": "inexact",
- "versions": [
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- ]
- }
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- "version": "0.19.5+galaxy1"
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
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- "state": "missing"
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- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -56423,23 +47264,22 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
- ]
+ "state": "exact",
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.23.2+galaxy0"
+ ]
},
{
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "0.20.1+galaxy0",
+ "0.23.2+galaxy0"
]
},
{
@@ -56462,15 +47302,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "2.27+galaxy0"
+ "0.23.4+galaxy0"
]
},
{
@@ -56500,74 +47336,47 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "2.17+galaxy1"
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.26+galaxy0"
+ "0.23.2+galaxy0"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "2.17+galaxy1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.24+galaxy0",
- "2.28+galaxy0",
- "2.27+galaxy0",
- "2.12",
- "2.26+galaxy0",
- "2.23+galaxy0",
- "2.17+galaxy2",
- "2.22+galaxy0"
- ]
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "2.24+galaxy0",
- "2.17+galaxy0"
- ]
+ "state": "exact",
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://usegalaxy.org",
- "state": "inexact",
- "versions": [
- "2.24+galaxy0",
- "2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4",
- "2.27+galaxy0",
- "2.17",
- "2.26+galaxy0",
- "2.20+galaxy2",
- "2.23+galaxy0",
- "2.17+galaxy2",
- "2.17+galaxy3",
- "2.20+galaxy1"
- ]
+ "state": "exact",
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "2.17+galaxy1"
+ "version": "0.19.5+galaxy1"
},
{
"server": "https://viralvariant.anses.fr/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.23.2+galaxy0"
+ ]
}
],
- "version": "2.17+galaxy1"
+ "version": "0.19.5+galaxy1"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -56589,6 +47398,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -56611,8 +47424,11 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "1.7"
+ "state": "inexact",
+ "versions": [
+ "2.28+galaxy0",
+ "2.24+galaxy0"
+ ]
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -56620,8 +47436,12 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.7"
+ "state": "inexact",
+ "versions": [
+ "2.28+galaxy0",
+ "2.17+galaxy4",
+ "2.17+galaxy0"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -56643,15 +47463,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "1.11+galaxy1"
+ "2.27+galaxy0"
]
},
{
@@ -56676,58 +47492,65 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1"
- ]
+ "state": "missing"
},
{
"server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "1.9",
- "1.8+galaxy0"
- ]
+ "state": "exact",
+ "version": "2.17+galaxy1"
},
{
"server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.7"
+ "state": "inexact",
+ "versions": [
+ "2.26+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.7"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7"
+ "version": "2.17+galaxy1"
},
{
"server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "1.7"
+ "state": "inexact",
+ "versions": [
+ "2.24+galaxy0",
+ "2.17+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.7"
+ "state": "inexact",
+ "versions": [
+ "2.28+galaxy0",
+ "2.24+galaxy0",
+ "2.17+galaxy4",
+ "2.17+galaxy0",
+ "2.27+galaxy0",
+ "2.17",
+ "2.26+galaxy0",
+ "2.20+galaxy1",
+ "2.17+galaxy3",
+ "2.20+galaxy2",
+ "2.17+galaxy2",
+ "2.23+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "1.7"
+ "version": "2.17+galaxy1"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.7"
+ "version": "2.17+galaxy1"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -56749,6 +47572,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -56771,24 +47598,17 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "1.42.0+galaxy0"
- ]
+ "state": "exact",
+ "version": "1.7"
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "inexact",
- "versions": [
- "1.43.0+galaxy0"
- ]
+ "state": "missing"
},
{
"server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
- "1.28.2+galaxy1"
- ]
+ "state": "exact",
+ "version": "1.7"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -56810,15 +47630,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "1.42.0+galaxy0"
+ "1.11+galaxy1"
]
},
{
@@ -56843,61 +47659,53 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1"
+ ]
},
{
"server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.25.0+galaxy1"
- },
- {
- "server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.41.0+galaxy0"
+ "1.9",
+ "1.8+galaxy0"
]
},
{
- "server": "https://usegalaxy.eu",
+ "server": "https://usegalaxy.cz/",
"state": "exact",
- "version": "1.25.0+galaxy1"
+ "version": "1.7"
},
{
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.42.0+galaxy0",
- "1.43.0+galaxy0",
- "1.28.2+galaxy1",
- "1.41.0+galaxy0",
- "1.42.0+galaxy1",
- "1.36.2+galaxy1"
- ]
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.7"
},
{
"server": "https://usegalaxy.no/",
"state": "exact",
- "version": "1.25.0+galaxy1"
+ "version": "1.7"
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "1.25.0+galaxy1"
+ "version": "1.7"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "1.25.0+galaxy1"
+ "version": "1.7"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.25.0+galaxy1"
+ "version": "1.7"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -56919,6 +47727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -56941,18 +47753,23 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "1.9+galaxy1"
+ "state": "inexact",
+ "versions": [
+ "1.42.0+galaxy0"
+ ]
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "1.43.0+galaxy0"
+ ]
},
{
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.13"
+ "1.28.2+galaxy1"
]
},
{
@@ -56975,15 +47792,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2"
+ "1.42.0+galaxy0"
]
},
{
@@ -57013,49 +47826,44 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.15.1+galaxy0"
+ "1.41.0+galaxy0"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.9+galaxy1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
"server": "https://usegalaxy.no/",
"state": "exact",
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.9+galaxy1"
+ "version": "1.25.0+galaxy1"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -57077,6 +47885,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -57099,11 +47911,8 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "1.15.1+galaxy2",
- "1.9"
- ]
+ "state": "exact",
+ "version": "1.9+galaxy1"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -57113,7 +47922,7 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.9+galaxy3"
+ "1.13"
]
},
{
@@ -57136,10 +47945,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -57189,7 +47994,158 @@
"version": "1.9+galaxy1"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.9+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.9+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.9+galaxy1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.9+galaxy1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "https://palfinder.ls.manchester.ac.uk/",
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+ "state": "missing"
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+ "server": "https://galaxy.bio.di.uminho.pt/",
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+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.9+galaxy1"
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+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "1.15.1+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.9+galaxy1"
},
@@ -57238,6 +48194,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -57292,10 +48252,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -57342,11 +48298,6 @@
"state": "exact",
"version": "1.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.2"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -57393,6 +48344,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -57448,10 +48403,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -57498,28 +48449,6 @@
"state": "exact",
"version": "2.10.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "2.10.4",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.8+galaxy0",
- "3.0.5+galaxy0",
- "2.10.7+galaxy2",
- "3.0.3+galaxy0",
- "2.11.0+galaxy1",
- "3.1.1+galaxy1",
- "3.0.8+galaxy0",
- "3.1.0+galaxy1",
- "3.0.10+galaxy0",
- "3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -57567,6 +48496,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -57620,10 +48553,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -57672,11 +48601,6 @@
"state": "exact",
"version": "0.4.8.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.8.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -57722,6 +48646,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -57778,10 +48706,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -57831,14 +48755,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -57907,7 +48823,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 368,
- "visitors": 2247111,
+ "visitors": 2257953,
"workflows": [
{
"creators": [],
@@ -57993,7 +48909,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Samtools fastx\"];\n 7 -->|outputsam| 10;\n 11[\"Samtools fastx\"];\n 9 -->|outputsam| 11;\n 12[\"Collapse Collection\"];\n 10 -->|nonspecific| 12;\n 13[\"Zip Collection\"];\n 11 -->|forward| 13;\n 11 -->|reverse| 13;\n 14[\"Collapse Collection\"];\n 11 -->|forward| 14;\n 15[\"Collapse Collection\"];\n 11 -->|reverse| 15;\n 16[\"seqtk_sample\"];\n 14 -->|output| 16;\n 17[\"seqtk_sample\"];\n 15 -->|output| 17;\n 18[\"Create assemblies with Unicycler\"];\n 12 -->|output| 18;\n 16 -->|default| 18;\n 17 -->|default| 18;\n 19[\"Bandage Info\"];\n 18 -->|assembly_graph| 19;\n 2[\"fastp: Trimmed Illumina Reads\"];\n 0 -->|output| 2;\n 20[\"Filter sequences by length\"];\n 18 -->|assembly| 20;\n 21[\"Bandage Image\"];\n 18 -->|assembly_graph| 21;\n 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 4[\"Map with minimap2\"];\n 1 -->|output| 4;\n 5[\"MultiQC\"];\n 2 -->|report_json| 5;\n 6[\"Bowtie2\"];\n 2 -->|output_paired_coll| 6;\n 7[\"Samtools view\"];\n 4 -->|alignment_output| 7;\n 8[\"Samtools stats\"];\n 4 -->|alignment_output| 8;\n 9[\"Samtools view\"];\n 6 -->|output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "assembly_with_preprocessing",
"outputs": [
{
@@ -58919,7 +49835,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Samtools stats\"];\n 6 -->|alignment_output| 10;\n 11[\"Samtools view\"];\n 8 -->|output| 11;\n 12[\"Samtools fastx\"];\n 9 -->|outputsam| 12;\n 13[\"Samtools fastx\"];\n 11 -->|outputsam| 13;\n 14[\"Collapse Collection\"];\n 12 -->|nonspecific| 14;\n 15[\"Zip Collection\"];\n 13 -->|forward| 15;\n 13 -->|reverse| 15;\n 16[\"Collapse Collection\"];\n 13 -->|forward| 16;\n 17[\"Collapse Collection\"];\n 13 -->|reverse| 17;\n 18[\"seqtk_sample\"];\n 16 -->|output| 18;\n 19[\"seqtk_sample\"];\n 17 -->|output| 19;\n 2[\"Illumina data\"];\n 0 -->|output| 2;\n 20[\"Create assemblies with Unicycler\"];\n 14 -->|output| 20;\n 18 -->|default| 20;\n 19 -->|default| 20;\n 21[\"Bandage Info\"];\n 20 -->|assembly_graph| 21;\n 22[\"Bandage Image\"];\n 20 -->|assembly_graph| 22;\n 23[\"Filter sequences by length\"];\n 20 -->|assembly| 23;\n 3[\"ONT data\"];\n 1 -->|output| 3;\n 4[\"fastp: Trimmed Illumina Reads\"];\n 2 -->|list_paired| 4;\n 5[\"NanoPlot\"];\n 3 -->|output_collection| 5;\n 6[\"Map with minimap2\"];\n 3 -->|output_collection| 6;\n 7[\"MultiQC\"];\n 4 -->|report_json| 7;\n 8[\"Bowtie2\"];\n 4 -->|output_paired_coll| 8;\n 9[\"Samtools view\"];\n 6 -->|alignment_output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "assembly_with_preprocessing_and_sra_download",
"outputs": [
{
@@ -60191,30 +51107,6 @@
},
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{
"email": "delphine.lariviere@galaxy.org",
@@ -60292,181 +51184,38 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
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- "gallantries",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
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@@ -60478,12 +51227,12 @@
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],
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@@ -62199,6 +52911,10 @@
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"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -62256,10 +52972,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -62295,9 +53007,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -62305,8 +53017,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -62315,11 +53027,6 @@
"state": "exact",
"version": "1.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -62365,6 +53072,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -62425,10 +53136,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -62462,9 +53169,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -62478,11 +53185,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -62528,6 +53230,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -62588,10 +53294,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -62629,10 +53331,10 @@
"2.27.0.0",
"2.29.2",
"2.31.1+galaxy0",
+ "2.29.0",
"2.24.0",
"2.19.0",
- "2.30.0",
- "2.29.0"
+ "2.30.0"
]
},
{
@@ -62645,11 +53347,6 @@
"state": "exact",
"version": "2.30.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -62695,6 +53392,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -62747,10 +53448,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -62793,10 +53490,6 @@
"state": "exact",
"version": "1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -62841,6 +53534,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -62893,10 +53590,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -62939,10 +53632,6 @@
"state": "exact",
"version": "1.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -62987,6 +53676,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63040,10 +53733,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -63091,11 +53780,6 @@
"state": "exact",
"version": "5.2.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -63141,6 +53825,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63173,10 +53861,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -63199,10 +53887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -63250,23 +53934,18 @@
"state": "exact",
"version": "5.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -63309,6 +53988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63362,10 +54045,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -63409,13 +54088,6 @@
"state": "exact",
"version": "2.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -63460,6 +54132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63515,10 +54191,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -63562,11 +54234,6 @@
"state": "exact",
"version": "2.2.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -63611,6 +54278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63664,10 +54335,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -63712,11 +54379,6 @@
"state": "exact",
"version": "0.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -63762,6 +54424,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63817,10 +54483,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -63865,11 +54527,6 @@
"state": "exact",
"version": "2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -63917,6 +54574,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -63970,10 +54631,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64016,11 +54673,6 @@
"state": "exact",
"version": "2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -64066,6 +54718,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64118,10 +54774,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64154,8 +54806,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -64168,11 +54820,6 @@
"state": "exact",
"version": "0.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -64218,6 +54865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64270,10 +54921,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64310,8 +54957,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.3+galaxy3",
- "1.3+galaxy2"
+ "1.3+galaxy2",
+ "1.3+galaxy3"
]
},
{
@@ -64319,15 +54966,6 @@
"state": "exact",
"version": "1.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.3+galaxy3",
- "1.3+galaxy2",
- "1.3+galaxy4"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -64372,6 +55010,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64424,10 +55066,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64470,11 +55108,6 @@
"state": "exact",
"version": "1.3+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -64519,6 +55152,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64551,8 +55188,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -64575,10 +55212,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64623,11 +55256,6 @@
"state": "exact",
"version": "1.3+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -64672,6 +55300,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64704,8 +55336,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -64728,10 +55360,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -64774,11 +55402,6 @@
"state": "exact",
"version": "1.3+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy6"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -64823,6 +55446,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -64847,8 +55474,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
+ "2.28+galaxy0",
+ "2.24+galaxy0"
]
},
{
@@ -64880,10 +55507,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -64920,12 +55543,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -64940,20 +55563,6 @@
"state": "exact",
"version": "2.17+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.24+galaxy0",
- "2.28+galaxy0",
- "2.27+galaxy0",
- "2.12",
- "2.26+galaxy0",
- "2.23+galaxy0",
- "2.17+galaxy2",
- "2.22+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -65002,6 +55611,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65036,8 +55649,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -65060,10 +55673,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -65100,12 +55709,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -65120,11 +55729,6 @@
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},
- {
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- "state": "exact",
- "version": "2.24+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -65170,6 +55774,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65222,10 +55830,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -65268,10 +55872,6 @@
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -65316,6 +55916,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65368,10 +55972,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -65414,10 +56014,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -65462,6 +56058,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65514,10 +56114,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -65562,10 +56158,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -65610,6 +56202,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65662,10 +56258,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -65708,10 +56300,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -65756,6 +56344,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65780,8 +56372,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
- "5.2.0+galaxy1"
+ "5.2.0+galaxy1",
+ "5.0.2+galaxy0"
]
},
{
@@ -65813,10 +56405,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -65855,8 +56443,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -65869,11 +56457,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.2+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -65919,6 +56502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -65974,10 +56561,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -66025,10 +56608,6 @@
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{
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"state": "missing"
@@ -66072,6 +56651,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -66124,10 +56707,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -66170,10 +56749,6 @@
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},
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{
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"state": "missing"
@@ -66218,6 +56793,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -66257,8 +56836,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
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- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -66281,10 +56860,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
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@@ -66327,8 +56902,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
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+ "1.16.1",
+ "1.6"
]
},
{
@@ -66343,11 +56918,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "3.5+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -66367,16 +56937,16 @@
"1.16.3",
"1.16.5",
"1.16.1",
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+ "4.0+galaxy1",
"3.4+galaxy2",
+ "3.7+galaxy0",
"3.4+galaxy1",
"4.6+galaxy1",
"3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
"4.9+galaxy0",
- "4.0+galaxy1",
"3.5+galaxy1",
+ "3.5+galaxy0",
+ "4.8+galaxy0",
"1.16.6"
]
},
@@ -66415,6 +56985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -66454,8 +57028,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -66478,10 +57052,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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@@ -66522,8 +57092,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
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"state": "exact",
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},
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- "state": "exact",
- "version": "4.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -66588,6 +57153,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -66644,10 +57213,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -66697,14 +57262,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -66750,6 +57307,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -66804,10 +57365,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -66855,11 +57412,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "5.1.0"
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{
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"state": "exact",
@@ -66881,148 +57433,6 @@
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- "state": "missing"
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- {
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- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- "server": "https://usegalaxy.eu",
- "state": "missing"
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- "server": "https://usegalaxy.fr/",
- "state": "missing"
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- "server": "https://usegalaxy.no/",
- "state": "missing"
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- "server": "https://usegalaxy.org",
- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "version": "2.2.1+galaxy1"
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]
},
@@ -67074,8 +57484,7 @@
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"toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
- "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
- "ttoolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1"
+ "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
],
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"topic_name_human": "Assembly",
@@ -67092,12 +57501,12 @@
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"slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json"
},
- "version": 54,
+ "version": 55,
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 118,
- "visitors": 11946,
+ "visit_duration": 120,
+ "visitors": 12032,
"workflows": [
{
"creators": [],
@@ -67275,7 +57684,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"GFA to FASTA\"];\n 5[\"GFA to FASTA\"];\n 6[\"Cutadapt\"];\n 3 -->|output| 6;\n 7[\"Busco\"];\n 4 -->|out_fa| 7;\n 8[\"Busco\"];\n 5 -->|out_fa| 8;\n 9[\"Purge overlaps\"];\n 5 -->|out_fa| 9;\n 10[\"Collapse Collection\"];\n 6 -->|out1| 10;\n 11[\"Meryl\"];\n 6 -->|out1| 11;\n 12[\"Map with minimap2\"];\n 6 -->|out1| 12;\n 5 -->|out_fa| 12;\n 13[\"Quast\"];\n 5 -->|out_fa| 13;\n 4 -->|out_fa| 13;\n 6 -->|out1| 13;\n 14[\"Map with minimap2\"];\n 9 -->|split_fasta| 14;\n 9 -->|split_fasta| 14;\n 15[\"Meryl\"];\n 11 -->|read_db| 15;\n 16[\"Purge overlaps\"];\n 12 -->|alignment_output| 16;\n 17[\"Meryl\"];\n 15 -->|read_db| 17;\n 18[\"Merqury\"];\n 5 -->|out_fa| 18;\n 4 -->|out_fa| 18;\n 15 -->|read_db| 18;\n 19[\"Purge overlaps\"];\n 16 -->|pbcstat_cov| 19;\n 16 -->|calcuts_cutoff| 19;\n 14 -->|alignment_output| 19;\n 20[\"GenomeScope\"];\n 17 -->|read_db_hist| 20;\n 21[\"Purge overlaps\"];\n 19 -->|purge_dups_bed| 21;\n 5 -->|out_fa| 21;\n 22[\"Replace\"];\n 20 -->|summary| 22;\n 23[\"Compute\"];\n 20 -->|model_params| 23;\n 24[\"Bionano Hybrid Scaffold\"];\n 0 -->|output| 24;\n 21 -->|get_seqs_purged| 24;\n 25[\"Concatenate datasets\"];\n 21 -->|get_seqs_hap| 25;\n 4 -->|out_fa| 25;\n 26[\"Busco\"];\n 21 -->|get_seqs_purged| 26;\n 27[\"Replace\"];\n 22 -->|outfile| 27;\n 28[\"Compute\"];\n 23 -->|out_file1| 28;\n 29[\"Concatenate datasets\"];\n 24 -->|ngs_contigs_scaffold_trimmed| 29;\n 24 -->|ngs_contigs_not_scaffolded_trimmed| 29;\n 30[\"Purge overlaps\"];\n 25 -->|out_file1| 30;\n 31[\"Map with minimap2\"];\n 10 -->|output| 31;\n 25 -->|out_file1| 31;\n 32[\"Search in textfiles\"];\n 27 -->|outfile| 32;\n 33[\"Advanced Cut\"];\n 28 -->|out_file1| 33;\n 34[\"Advanced Cut\"];\n 28 -->|out_file1| 34;\n 35[\"BWA-MEM2\"];\n 1 -->|output| 35;\n 29 -->|out_file1| 35;\n 36[\"BWA-MEM2\"];\n 2 -->|output| 36;\n 29 -->|out_file1| 36;\n 37[\"Replace\"];\n 29 -->|out_file1| 37;\n 38[\"Quast\"];\n 29 -->|out_file1| 38;\n 10 -->|output| 38;\n 39[\"Busco\"];\n 29 -->|out_file1| 39;\n 40[\"Map with minimap2\"];\n 30 -->|split_fasta| 40;\n 30 -->|split_fasta| 40;\n 41[\"Purge overlaps\"];\n 31 -->|alignment_output| 41;\n 42[\"Convert\"];\n 32 -->|output| 42;\n 43[\"Filter and merge\"];\n 36 -->|bam_output| 43;\n 35 -->|bam_output| 43;\n 44[\"Purge overlaps\"];\n 41 -->|pbcstat_cov| 44;\n 41 -->|calcuts_cutoff| 44;\n 40 -->|alignment_output| 44;\n 45[\"Advanced Cut\"];\n 42 -->|out_file1| 45;\n 46[\"bedtools BAM to BED\"];\n 43 -->|outfile| 46;\n 47[\"PretextMap\"];\n 43 -->|outfile| 47;\n 48[\"Purge overlaps\"];\n 44 -->|purge_dups_bed| 48;\n 25 -->|out_file1| 48;\n 49[\"Sort\"];\n 46 -->|output| 49;\n 50[\"Pretext Snapshot\"];\n 47 -->|pretext_map_out| 50;\n 51[\"Busco\"];\n 48 -->|get_seqs_purged| 51;\n 52[\"Quast\"];\n 21 -->|get_seqs_purged| 52;\n 48 -->|get_seqs_purged| 52;\n 10 -->|output| 52;\n 53[\"SALSA\"];\n 49 -->|out_file1| 53;\n 37 -->|outfile| 53;\n 54[\"BWA-MEM2\"];\n 1 -->|output| 54;\n 53 -->|scaffolds_fasta| 54;\n 55[\"BWA-MEM2\"];\n 2 -->|output| 55;\n 53 -->|scaffolds_fasta| 55;\n 56[\"Busco\"];\n 53 -->|scaffolds_fasta| 56;\n 57[\"Quast\"];\n 53 -->|scaffolds_fasta| 57;\n 10 -->|output| 57;\n 58[\"Filter and merge\"];\n 55 -->|bam_output| 58;\n 54 -->|bam_output| 58;\n 59[\"PretextMap\"];\n 58 -->|outfile| 59;\n 60[\"Pretext Snapshot\"];\n 59 -->|pretext_map_out| 60;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "VGP assembly: training workflow",
"outputs": [],
"parent_id": "assembly/vgp_genome_assembly",
@@ -67559,7 +57968,7 @@
"Identify contaminant species",
"Remove Mitochondrial DNA from an assembly"
],
- "pageviews": 384,
+ "pageviews": 403,
"pub_date": "2024-09-04",
"questions": [
"How to remove contaminant sequences from your assembly?"
@@ -67581,15 +57990,15 @@
],
"short_id": "T00452",
"short_tools": [
- "parse_mito_blast",
- "tp_cat",
- "gfastats",
- "Filter1",
- "ncbi_dustmasker_wrapper",
"tp_sed_tool",
- "Cut1",
"kraken2",
- "ncbi_blastn_wrapper"
+ "Filter1",
+ "Cut1",
+ "tp_cat",
+ "parse_mito_blast",
+ "ncbi_blastn_wrapper",
+ "ncbi_dustmasker_wrapper",
+ "gfastats"
],
"slides": false,
"slides_recordings": false,
@@ -67641,6 +58050,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -67696,10 +58109,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -67746,11 +58155,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -67795,6 +58199,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -67847,10 +58255,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -67891,10 +58295,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -67937,6 +58337,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -67989,10 +58393,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -68033,10 +58433,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -68079,6 +58475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68132,10 +58532,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -68178,10 +58574,6 @@
"state": "exact",
"version": "1.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -68226,6 +58618,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68280,10 +58676,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -68332,11 +58724,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -68382,6 +58769,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68406,8 +58797,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -68418,8 +58809,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -68442,10 +58833,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -68486,8 +58873,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -68495,17 +58882,12 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -68548,6 +58930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68602,10 +58988,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -68652,11 +59034,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -68702,6 +59079,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68760,10 +59141,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -68815,11 +59192,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -68868,6 +59240,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -68905,9 +59281,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.10.1+galaxy1",
"2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.10.1+galaxy1"
]
},
{
@@ -68930,10 +59306,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -68976,9 +59348,9 @@
"0.3.1",
"2.14.1+galaxy2",
"0.3.3",
- "0.3.0",
+ "0.1.07",
"0.0.11",
- "0.1.07"
+ "0.3.0"
]
},
{
@@ -68987,17 +59359,17 @@
"versions": [
"2.10.1+galaxy2",
"0.1.07",
- "0.0.22",
"0.1.06",
- "0.0.20",
- "0.0.19",
- "0.2.00",
- "0.0.14",
+ "0.1.04",
+ "0.1.00",
"0.1.08",
"0.2.01",
- "0.1.04",
- "0.1.01",
- "0.1.00"
+ "0.2.00",
+ "0.0.14",
+ "0.0.19",
+ "0.0.20",
+ "0.0.22",
+ "0.1.01"
]
},
{
@@ -69005,11 +59377,6 @@
"state": "exact",
"version": "2.14.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.14.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -69057,6 +59424,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -69115,10 +59486,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -69165,17 +59532,17 @@
"versions": [
"2.10.1+galaxy2",
"0.1.07",
- "0.0.22",
"0.1.06",
- "0.0.20",
- "0.0.19",
- "0.2.00",
- "0.0.14",
+ "0.1.04",
+ "0.1.00",
"0.1.08",
"0.2.01",
- "0.1.04",
- "0.1.01",
- "0.1.00"
+ "0.2.00",
+ "0.0.14",
+ "0.0.19",
+ "0.0.20",
+ "0.0.22",
+ "0.1.01"
]
},
{
@@ -69183,11 +59550,6 @@
"state": "exact",
"version": "2.14.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.14.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -69235,6 +59597,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -69260,8 +59626,8 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.10.1+galaxy0",
- "2.10.1+galaxy2"
+ "2.10.1+galaxy2",
+ "2.10.1+galaxy0"
]
},
{
@@ -69273,8 +59639,8 @@
"state": "inexact",
"versions": [
"2.10.1+galaxy1",
- "2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.14.1+galaxy2"
]
},
{
@@ -69297,10 +59663,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -69341,10 +59703,10 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.14.1+galaxy2",
"0.3.3",
- "0.1.07",
- "0.3.0"
+ "2.14.1+galaxy2",
+ "0.3.0",
+ "0.1.07"
]
},
{
@@ -69353,14 +59715,14 @@
"versions": [
"2.10.1+galaxy2",
"0.1.07",
- "0.2.01",
- "0.1.08",
- "0.1.04",
+ "0.1.00",
+ "0.1.06",
"0.0.22",
- "0.2.00",
"0.1.01",
- "0.1.06",
- "0.1.00"
+ "0.2.00",
+ "0.1.04",
+ "0.2.01",
+ "0.1.08"
]
},
{
@@ -69368,11 +59730,6 @@
"state": "exact",
"version": "2.14.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.14.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -69421,178 +59778,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "0.3.1",
- "2.10.1+galaxy0",
- "2.10.1+galaxy2"
- ]
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "2.14.1+galaxy2"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "2.14.1+galaxy2"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
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- "state": "inexact",
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- ]
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- "servers": [
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- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -69617,8 +59803,12 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "2.1.1+galaxy1"
+ "state": "inexact",
+ "versions": [
+ "0.3.1",
+ "2.10.1+galaxy2",
+ "2.10.1+galaxy0"
+ ]
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -69627,7 +59817,7 @@
{
"server": "https://galaxytrakr.org/",
"state": "exact",
- "version": "2.1.1+galaxy1"
+ "version": "2.14.1+galaxy2"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -69650,7 +59840,169 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "inexact",
+ "versions": [
+ "2.14.1+galaxy1"
+ ]
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "inexact",
+ "versions": [
+ "2.10.1+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.10.1+galaxy2",
+ "0.1.07",
+ "0.1.00",
+ "0.1.06",
+ "0.0.22",
+ "0.1.01",
+ "0.2.00",
+ "0.1.04",
+ "0.2.01",
+ "0.1.08"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "2.10.1+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "2.14.1+galaxy2"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "2.1.1+galaxy1"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "2.1.1+galaxy1"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -69686,8 +60038,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -69700,11 +60052,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -69750,6 +60097,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -69804,10 +60155,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -69843,8 +60190,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -69859,11 +60206,6 @@
"state": "exact",
"version": "2.1.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -69913,6 +60255,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -69965,10 +60311,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -70011,10 +60353,6 @@
"state": "exact",
"version": "1.0.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -70076,8 +60414,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 175,
- "visitors": 308,
+ "visit_duration": 192,
+ "visitors": 324,
"workflows": [
{
"creators": [
@@ -70184,7 +60522,7 @@
],
"license": "BSD-3-Clause",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nScaffolded assembly fasta\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nDatabase for Kraken2\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"soft-masking \"];\n 0 -->|output| 2;\n 3[\"hard-masking\"];\n 2 -->|outfile| 3;\n 4[\"ID non-target contaminants\"];\n 1 -->|output| 4;\n 3 -->|output| 4;\n c380857b-5180-4e82-a14f-8b575f10abaa[\"Output\\nKraken2 classification scores\"];\n 4 --> c380857b-5180-4e82-a14f-8b575f10abaa;\n style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;\n 5[\"blast mitochondria DB\"];\n 3 -->|output| 5;\n 6[\"Cut\"];\n 4 -->|output| 6;\n 7[\"parsing blast output\"];\n 5 -->|output1| 7;\n 1478af1e-52f4-48fe-b966-0a61e2014a58[\"Output\\nmito_scaff_names\"];\n 7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;\n style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;\n 8[\"Filter\"];\n 6 -->|out_file1| 8;\n 64156e28-aaf0-4578-9a7e-d6d21774c2c8[\"Output\\ncontaminants_table\"];\n 8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;\n style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;\n 9[\"Cut\"];\n 8 -->|out_file1| 9;\n 10[\"concatenate scaffold lists\"];\n 7 -->|mito_scaff_names| 10;\n 9 -->|out_file1| 10;\n 77084ec5-a145-40c1-9cfc-476d091105ae[\"Output\\nfull contaminant + mito scaffold list\"];\n 10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;\n style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;\n 11[\"removing scaffolds \"];\n 0 -->|output| 11;\n 10 -->|out_file1| 11;\n 88a8e9ed-d92c-4340-aaad-c6d450a336aa[\"Output\\nfinal decontaminated assembly\"];\n 11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;\n style 88a8e9ed-d92c-4340-aaad-c6d450a336aa stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assembly-decontamination-VGP9",
"outputs": [
{
@@ -70693,24 +61031,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n owner: bgruening\n revisions: 7d9ee8cd14b8\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n owner: bgruening\n revisions: '392811378515'\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n owner: bgruening\n revisions: e8ac2b53f262\n tool_panel_section_label: NCBI Blast\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n owner: bgruening\n revisions: 5799092ffdff\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n owner: bgruening\n revisions: 3ef480892a9f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n owner: devteam\n revisions: 3a0efe14891f\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n owner: galaxy-australia\n revisions: 5e0825476fb7\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: ddddce450736\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n owner: iuc\n revisions: 25ca5d73aedf\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: bb935709506a\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 2babe6d5c561\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n owner: iuc\n revisions: b4a22d90cce9\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n owner: iuc\n revisions: 01210c4e9144\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n owner: iuc\n revisions: f8113c25bc6b\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n owner: iuc\n revisions: 29dabd8db6f2\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n owner: iuc\n revisions: 5cc34c3f440d\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n owner: iuc\n revisions: dfb8a4497339\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n owner: iuc\n revisions: c6cec5ab35c1\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n owner: iuc\n revisions: 44c66e8d21e6\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 90981f86000f\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
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- "GitFab93",
- "gallardoalba",
- "tbrown91",
- "delphine-l"
- ],
- "reviewing": [
- "teresa-m",
- "delphine-l",
- "bgruening",
- "tbrown91",
- "SaimMomin12",
- "shiltemann",
- "deeptivarshney",
- "gallardoalba"
- ]
- },
"contributors": [
{
"id": "GitFab93",
@@ -70749,158 +61069,24 @@
"orcid": "0000-0001-6421-3484",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
- {
- "email": "delphine.lariviere@galaxy.org",
- "id": "delphine-l",
- "joined": "2017-09",
- "name": "Delphine Lariviere",
- "orcid": "0000-0001-6421-3484",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "brown@izw-berlin.de",
- "id": "tbrown91",
- "joined": "2024-08",
- "name": "Tom Brown",
- "orcid": "0000-0001-8293-4816",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "email": "momins@informatik.uni-freiburg.de",
- "id": "SaimMomin12",
- "joined": "2024-03",
- "linkedin": "saim-momin",
- "matrix": "saimmomin:matrix.org",
- "name": "Saim Momin",
- "orcid": "0009-0003-9935-828X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/SaimMomin12/",
- "twitter": "SaimMomin12",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/SaimMomin12.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "deeptivarshney",
- "joined": "2022-12",
- "name": "Deepti Varshney",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
}
],
"dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
"edam_operation": [
- "Data handling",
+ "Pairwise sequence alignment",
"Genome assembly",
- "Genotyping",
+ "Sequence assembly validation",
+ "Sequence assembly visualisation",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Phasing",
+ "Data handling",
"Sequence alignment analysis",
- "Pairwise sequence alignment",
+ "k-mer counting",
"Sequence alignment",
"De-novo assembly",
"Sequence trimming",
- "Sequence assembly validation",
- "k-mer counting",
- "Phasing",
- "Sequence assembly visualisation",
- "Transcriptome assembly",
- "Scaffolding"
+ "Genotyping"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -70929,7 +61115,7 @@
"Apply the post-assembly-QC-workflow using the necessary tools",
"Analyse and evaluate the results of the workflow"
],
- "pageviews": 1465,
+ "pageviews": 1496,
"pub_date": "2023-06-23",
"questions": [
"What combination of tools can assess the quality of a genome assembly?",
@@ -70953,26 +61139,26 @@
],
"short_id": "T00355",
"short_tools": [
- "gfastats",
- "minimap2",
- "bellerophon",
- "CONVERTER_gz_to_uncompressed",
+ "genomescope",
"meryl",
- "busco",
+ "CONVERTER_gz_to_uncompressed",
+ "pretext_map",
+ "__EXTRACT_DATASET__",
"smudgeplot",
- "bg_diamond",
- "bandage_image",
- "genomescope",
- "collapse_dataset",
"bwa_mem2",
- "interactive_tool_blobtoolkit",
+ "busco",
"blobtoolkit",
- "tp_find_and_replace",
- "pretext_map",
+ "bandage_image",
+ "minimap2",
"merqury",
- "__EXTRACT_DATASET__",
- "samtools_stats",
- "pretext_snapshot"
+ "bellerophon",
+ "gfastats",
+ "interactive_tool_blobtoolkit",
+ "collapse_dataset",
+ "bg_diamond",
+ "tp_find_and_replace",
+ "pretext_snapshot",
+ "samtools_stats"
],
"slides": false,
"slides_recordings": false,
@@ -71019,6 +61205,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -71074,10 +61264,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -71124,11 +61310,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -71173,6 +61354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -71225,10 +61410,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -71269,10 +61450,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -71315,6 +61492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -71367,10 +61548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -71411,10 +61588,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -71457,6 +61630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -71509,10 +61686,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -71553,10 +61726,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -71599,6 +61768,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -71651,10 +61824,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -71700,10 +61869,6 @@
"state": "exact",
"version": "3.4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -71754,6 +61919,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -71806,10 +61975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -71855,10 +62020,6 @@
"state": "exact",
"version": "4.0.7+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -71903,6 +62064,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -71962,10 +62127,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -72008,11 +62169,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -72058,6 +62214,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72114,10 +62274,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -72160,10 +62316,6 @@
"state": "exact",
"version": "1.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -72178,9 +62330,9 @@
"state": "inexact",
"versions": [
"1.3.6+galaxy0",
+ "1.3.5+galaxy2",
"1.3.5+galaxy0",
"1.3.4+galaxy0",
- "1.3.5+galaxy2",
"1.3.8+galaxy0",
"1.3.9+galaxy0"
]
@@ -72215,6 +62367,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72268,10 +62424,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -72314,10 +62466,6 @@
"state": "exact",
"version": "1.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -72362,6 +62510,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72416,10 +62568,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -72456,10 +62604,10 @@
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
"1.1.2",
+ "1.1.1",
"1.0.0",
- "1.1.1"
+ "1.1.0"
]
},
{
@@ -72472,18 +62620,13 @@
"state": "exact",
"version": "1.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
- "1.1.1"
+ "1.1.1",
+ "1.1.0"
]
},
{
@@ -72526,6 +62669,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72581,10 +62728,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -72622,8 +62765,8 @@
"versions": [
"2.0.2+galaxy2",
"2.0",
- "2.0.1",
"2.0.2",
+ "2.0.1",
"2.0.2+galaxy1"
]
},
@@ -72637,11 +62780,6 @@
"state": "exact",
"version": "2.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -72687,6 +62825,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72739,10 +62881,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -72787,10 +62925,6 @@
"state": "exact",
"version": "0.2.5+galaxy+2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -72841,6 +62975,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -72898,10 +63036,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -72951,11 +63085,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -73001,6 +63130,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73053,10 +63186,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -73099,10 +63228,6 @@
"state": "exact",
"version": "1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -73147,6 +63272,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73200,10 +63329,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -73251,41 +63376,36 @@
"state": "exact",
"version": "5.4.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.4.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "5.4.6+galaxy0",
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
+ "5.4.6+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "3.0.2+galaxy2",
- "4.1.2",
"5.3.2+galaxy0",
"5.5.0+galaxy0",
- "5.2.2+galaxy0",
+ "3.0.2+galaxy2",
+ "5.8.0+galaxy0",
"5.7.1+galaxy0",
- "5.8.0+galaxy0"
+ "4.1.2",
+ "5.2.2+galaxy0"
]
},
{
@@ -73323,6 +63443,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73355,10 +63479,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -73381,10 +63505,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -73432,23 +63552,18 @@
"state": "exact",
"version": "5.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -73491,6 +63606,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73544,10 +63663,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -73591,13 +63706,6 @@
"state": "exact",
"version": "2.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -73642,6 +63750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73695,10 +63807,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -73741,11 +63849,6 @@
"state": "exact",
"version": "2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -73791,6 +63894,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73843,10 +63950,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -73889,11 +63992,6 @@
"state": "exact",
"version": "1.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -73938,6 +64036,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -73970,8 +64072,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -73994,10 +64096,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -74040,11 +64138,6 @@
"state": "exact",
"version": "1.3+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy6"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -74089,6 +64182,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -74143,10 +64240,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -74183,12 +64276,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -74203,11 +64296,6 @@
"state": "exact",
"version": "2.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -74256,6 +64344,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -74308,10 +64400,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -74354,10 +64442,6 @@
"state": "exact",
"version": "0.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -74402,6 +64486,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -74454,10 +64542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -74502,10 +64586,6 @@
"state": "exact",
"version": "0.1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -74550,6 +64630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -74602,10 +64686,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -74648,10 +64728,6 @@
"state": "exact",
"version": "0.0.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -74696,6 +64772,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -74750,10 +64830,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -74801,11 +64877,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -74885,8 +64956,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 117,
- "visitors": 1119,
+ "visit_duration": 119,
+ "visitors": 1142,
"workflows": [
{
"creators": [
@@ -75209,7 +65280,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n style 5 fill:#ded,stroke:#393,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"Meryl\"];\n 3 -->|output| 9;\n 10[\"Collapse Collection\"];\n 3 -->|output| 10;\n 11[\"Create BlobtoolKit\"];\n 4 -->|output| 11;\n 0 -->|output| 11;\n 2 -->|output| 11;\n 1 -->|output| 11;\n 12[\"gfastats\"];\n 4 -->|output| 12;\n 13[\"Convert compressed file to uncompressed.\"];\n 4 -->|output| 13;\n 14[\"gfastats\"];\n 4 -->|output| 14;\n 15[\"Diamond\"];\n 4 -->|output| 15;\n 6 -->|output| 15;\n 16[\"Collapse Collection\"];\n 7 -->|output| 16;\n 17[\"Collapse Collection\"];\n 8 -->|output| 17;\n 18[\"Meryl\"];\n 9 -->|read_db| 18;\n 19[\"Map with minimap2\"];\n 10 -->|output| 19;\n 4 -->|output| 19;\n 20[\"Smudgeplot\"];\n 10 -->|output| 20;\n 21[\"Replace\"];\n 13 -->|output1| 21;\n 22[\"Bandage Image\"];\n 14 -->|output| 22;\n 23[\"BWA-MEM2\"];\n 16 -->|output| 23;\n 4 -->|output| 23;\n 24[\"BWA-MEM2\"];\n 17 -->|output| 24;\n 4 -->|output| 24;\n 25[\"Merqury\"];\n 4 -->|output| 25;\n 18 -->|read_db| 25;\n d2dbf498-5155-43b2-bf2a-ffed5c45100d[\"Output\\nMerqury on input dataset(s): stats\"];\n 25 --> d2dbf498-5155-43b2-bf2a-ffed5c45100d;\n style d2dbf498-5155-43b2-bf2a-ffed5c45100d stroke:#2c3143,stroke-width:4px;\n 0b43d206-253f-4c0b-a1f4-971402851c6d[\"Output\\nMerqury on input dataset(s): plots\"];\n 25 --> 0b43d206-253f-4c0b-a1f4-971402851c6d;\n style 0b43d206-253f-4c0b-a1f4-971402851c6d stroke:#2c3143,stroke-width:4px;\n 811a77e8-eb99-4dc7-9295-f0000fcb9fe5[\"Output\\nMerqury on input dataset(s): QV stats\"];\n 25 --> 811a77e8-eb99-4dc7-9295-f0000fcb9fe5;\n style 811a77e8-eb99-4dc7-9295-f0000fcb9fe5 stroke:#2c3143,stroke-width:4px;\n 26[\"Meryl\"];\n 18 -->|read_db| 26;\n 27[\"Samtools stats\"];\n 19 -->|alignment_output| 27;\n 28[\"Busco\"];\n 21 -->|outfile| 28;\n af98aae6-f1a3-493c-9cef-08e0926210d3[\"Output\\nBusco on input dataset(s): full table\"];\n 28 --> af98aae6-f1a3-493c-9cef-08e0926210d3;\n style af98aae6-f1a3-493c-9cef-08e0926210d3 stroke:#2c3143,stroke-width:4px;\n 929439b7-c688-45ea-848a-97c13d3e0028[\"Output\\nBusco on input dataset(s): short summary\"];\n 28 --> 929439b7-c688-45ea-848a-97c13d3e0028;\n style 929439b7-c688-45ea-848a-97c13d3e0028 stroke:#2c3143,stroke-width:4px;\n 29[\"Filter and merge\"];\n 24 -->|bam_output| 29;\n 23 -->|bam_output| 29;\n 30[\"Merqury plot 2\"];\n 25 -->|png_files| 30;\n 31[\"Merqury plot 1\"];\n 25 -->|png_files| 31;\n 32[\"Merqury plot 3\"];\n 25 -->|png_files| 32;\n 33[\"Merqury plot 5\"];\n 25 -->|png_files| 33;\n 34[\"Merqury plot 4\"];\n 25 -->|png_files| 34;\n 35[\"GenomeScope\"];\n 26 -->|read_db_hist| 35;\n 5 -->|output| 35;\n 36[\"BlobToolKit\"];\n 15 -->|blast_tabular| 36;\n 11 -->|blobdir| 36;\n 28 -->|busco_table| 36;\n 19 -->|alignment_output| 36;\n 37[\"PretextMap\"];\n 29 -->|outfile| 37;\n 38[\"BlobToolKit\"];\n 36 -->|blobdir| 38;\n 39[\"BlobToolKit\"];\n 36 -->|blobdir| 39;\n 40[\"BlobToolKit\"];\n 36 -->|blobdir| 40;\n 41[\"Pretext Snapshot\"];\n 37 -->|pretext_map_out| 41;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:14 +0000",
"name": "Post-assembly workflow",
"outputs": [
{
@@ -75804,27 +65875,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n owner: crs4\n revisions: bf68eb663bc3\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: b2f1f75d49c4\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n owner: iuc\n revisions: 59db8ea8c845\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n owner: iuc\n revisions: 9e3e80cc4ad4\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json",
- "contributions": {
- "authorship": [
- "nekrut",
- "delphine-l",
- "slugger70"
- ],
- "reviewing": [
- "shiltemann",
- "nsoranzo",
- "hexylena",
- "bgruening",
- "abretaud",
- "bebatut",
- "lecorguille",
- "afgane",
- "willdurand",
- "nekrut",
- "delphine-l",
- "njall"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -75853,217 +65903,6 @@
"orcid": "0000-0002-6100-4385",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
- },
- {
- "id": "afgane",
- "joined": "2018-06",
- "name": "Enis Afgan",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
- },
- {
- "id": "willdurand",
- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
- {
- "email": "anton@nekrut.org",
- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
- {
- "email": "delphine.lariviere@galaxy.org",
- "id": "delphine-l",
- "joined": "2017-09",
- "name": "Delphine Lariviere",
- "orcid": "0000-0001-6421-3484",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
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]
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"video_view": 0,
"visit_duration": 276,
- "visitors": 2253991,
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+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Unicycler training",
"outputs": [
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"logo": "GTN",
"mod_date": "2023-10-23",
- "pageviews": 4554011,
+ "pageviews": 4576988,
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@@ -78348,7 +68147,7 @@
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"visit_duration": 150,
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+ "pageviews": 6133506,
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"questions": [
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+ "climate_stripes",
"cds_essential_variability",
"tp_awk_tool",
+ "Grep1",
"datamash_ops",
- "climate_stripes",
"ggplot2_point",
"psy_maps"
],
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{
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{
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@@ -79152,6 +68754,10 @@
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"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79208,10 +68814,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -79261,11 +68863,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -79315,6 +68912,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79367,10 +68968,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -79413,10 +69010,6 @@
"state": "exact",
"version": "0.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -79460,6 +69053,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79512,10 +69109,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -79558,10 +69151,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -79607,6 +69196,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79659,10 +69252,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -79705,10 +69294,6 @@
"state": "exact",
"version": "1.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -79752,6 +69337,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79809,10 +69398,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -79859,11 +69444,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -79909,6 +69489,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -79965,10 +69549,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -80017,18 +69597,6 @@
"state": "exact",
"version": "2.2.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1+galaxy2",
- "3.4.0+galaxy1",
- "3.3.5+galaxy2",
- "3.3.5+galaxy1",
- "3.3.5+galaxy0",
- "3.4.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -80048,10 +69616,10 @@
"versions": [
"2.2.1+galaxy2",
"3.4.0+galaxy1",
- "3.3.5+galaxy2",
+ "3.4.0+galaxy0",
"3.3.5+galaxy1",
"3.3.5+galaxy0",
- "3.4.0+galaxy0"
+ "3.3.5+galaxy2"
]
},
{
@@ -80095,7 +69663,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 54,
- "visitors": 879,
+ "visitors": 882,
"workflows": [
{
"creators": [
@@ -80185,7 +69753,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Copernicus Essential Climate Variables\"];\n 3[\"climate stripes\"];\n 0 -->|output| 3;\n 4[\"Select\"];\n 1 -->|output| 4;\n 5[\"Datamash\"];\n 1 -->|output| 5;\n 6[\"Datamash\"];\n 1 -->|output| 6;\n 7[\"Datamash\"];\n 1 -->|output| 7;\n 8[\"Text reformatting\"];\n 1 -->|output| 8;\n 9[\"map plot\"];\n 2 -->|ofilename| 9;\n 10[\"Datamash\"];\n 8 -->|outfile| 10;\n 11[\"Datamash\"];\n 8 -->|outfile| 11;\n 12[\"Datamash\"];\n 10 -->|out_file| 12;\n 13[\"Datamash\"];\n 10 -->|out_file| 13;\n 14[\"Scatterplot w ggplot2\"];\n 11 -->|out_file| 14;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Climate 101",
"outputs": [],
"parent_id": "climate/climate-101",
@@ -80347,7 +69915,7 @@
"Handle going from one interactive tool to another",
"Learn to visualise gases around a volcano"
],
- "pageviews": 202,
+ "pageviews": 207,
"pub_date": "2024-01-26",
"questions": [
"How to visualise volcanoes with Sentinel 5 data ?",
@@ -80357,8 +69925,8 @@
"short_id": "T00396",
"short_tools": [
"interactive_tool_copernicus_notebook",
- "interactive_tool_panoply",
- "interactive_tool_copernicus"
+ "interactive_tool_copernicus",
+ "interactive_tool_panoply"
],
"slides": false,
"slides_recordings": false,
@@ -80388,6 +69956,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -80443,10 +70015,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -80493,11 +70061,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -80542,6 +70105,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -80594,10 +70161,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -80638,10 +70201,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -80684,6 +70243,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -80736,10 +70299,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -80780,10 +70339,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -80826,6 +70381,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -80878,10 +70437,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -80922,10 +70477,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -80979,8 +70530,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 33,
- "visitors": 174,
+ "visit_duration": 32,
+ "visitors": 179,
"workflows": [
{
"creators": [
@@ -81011,7 +70562,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Copernicus Data Space Ecosystem\"];\n 1[\"Panoply\"];\n 0 -->|output_collection| 1;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Sentinel5 volcanic data",
"outputs": [],
"parent_id": "climate/sentinel5_data",
@@ -81261,8 +70812,8 @@
"short_id": "T00376",
"short_tools": [
"interactive_tool_divand",
- "interactive_tool_odv",
- "divand_full_analysis"
+ "divand_full_analysis",
+ "interactive_tool_odv"
],
"slides": false,
"slides_recordings": false,
@@ -81298,6 +70849,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -81353,10 +70908,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -81403,11 +70954,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -81452,6 +70998,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -81505,7 +71055,141 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "missing"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "interactive_tool_odv",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -81548,10 +71232,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -81572,7 +71252,7 @@
"version": "local"
},
{
- "id": "interactive_tool_odv",
+ "id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -81595,145 +71275,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "local"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -81788,10 +71330,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -81833,10 +71371,6 @@
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+ "modified": "2024-12-13 13:26:15 +0000",
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{
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@@ -82323,110 +71845,6 @@
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@@ -82463,7 +71881,7 @@
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],
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],
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"climate_stripes",
+ "graphicsmagick_image_montage",
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"__MERGE_COLLECTION__",
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+ "ggplot2_point",
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"xarray_coords_info",
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- "xarray_netcdf2netcdf",
- "ggplot2_point"
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],
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"slides_recordings": false,
@@ -82549,6 +71967,10 @@
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"url": "https://hyperbrowser.uio.no/coloc-stats"
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+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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- "usegalaxy": false
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"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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"state": "local"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "inexact",
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+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
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+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ "state": "missing"
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+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ "state": "exact",
+ "version": "1.0.1"
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+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "1.0.3"
+ ]
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+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.0.1"
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+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.0.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.0.1"
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+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ ],
+ "version": "1.0.1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -84254,10 +73610,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -84306,11 +73658,6 @@
"state": "exact",
"version": "2.2.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -84374,7 +73721,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 342,
- "visitors": 1632554,
+ "visitors": 1642615,
"workflows": [
{
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@@ -84765,7 +74112,7 @@
],
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-->|output| 31;\n 6 -->|output| 31;\n 18 -->|output_netcdf| 31;\n 24 -->|output| 31;\n 32[\"NetCDF xarray map plotting\"];\n 28 -->|output| 32;\n 8 -->|output| 32;\n 18 -->|output_netcdf| 32;\n 24 -->|output| 32;\n 33[\"NetCDF xarray map plotting\"];\n 28 -->|output| 33;\n 5 -->|output| 33;\n 18 -->|output_netcdf| 33;\n 24 -->|output| 33;\n 34[\"NetCDF xarray map plotting\"];\n 28 -->|output| 34;\n 9 -->|output| 34;\n 18 -->|output_netcdf| 34;\n 24 -->|output| 34;\n 35[\"NetCDF xarray map plotting\"];\n 28 -->|output| 35;\n 4 -->|output| 35;\n 18 -->|output_netcdf| 35;\n 24 -->|output| 35;\n 36[\"NetCDF xarray map plotting\"];\n 28 -->|output| 36;\n 7 -->|output| 36;\n 18 -->|output_netcdf| 36;\n 24 -->|output| 36;\n 37[\"NetCDF xarray map plotting\"];\n 28 -->|output| 37;\n 3 -->|output| 37;\n 18 -->|output_netcdf| 37;\n 24 -->|output| 37;\n 38[\"NetCDF xarray map plotting\"];\n 28 -->|output| 38;\n 3 -->|output| 38;\n 18 -->|output_netcdf| 38;\n 24 -->|output| 38;\n 39[\"NetCDF xarray map plotting\"];\n 28 -->|output| 39;\n 4 -->|output| 39;\n 18 -->|output_netcdf| 39;\n 24 -->|output| 39;\n 40[\"NetCDF xarray map plotting\"];\n 28 -->|output| 40;\n 10 -->|output| 40;\n 18 -->|output_netcdf| 40;\n 24 -->|output| 40;\n 41[\"NetCDF xarray map plotting\"];\n 28 -->|output| 41;\n 5 -->|output| 41;\n 18 -->|output_netcdf| 41;\n 24 -->|output| 41;\n 42[\"NetCDF xarray map plotting\"];\n 28 -->|output| 42;\n 6 -->|output| 42;\n 18 -->|output_netcdf| 42;\n 24 -->|output| 42;\n 43[\"NetCDF xarray map plotting\"];\n 28 -->|output| 43;\n 10 -->|output| 43;\n 18 -->|output_netcdf| 43;\n 24 -->|output| 43;\n 44[\"NetCDF xarray map plotting\"];\n 28 -->|output| 44;\n 7 -->|output| 44;\n 18 -->|output_netcdf| 44;\n 24 -->|output| 44;\n 45[\"NetCDF xarray map plotting\"];\n 28 -->|output| 45;\n 9 -->|output| 45;\n 18 -->|output_netcdf| 45;\n 24 -->|output| 45;\n 46[\"NetCDF xarray map plotting\"];\n 28 -->|output| 46;\n 8 -->|output| 46;\n 18 -->|output_netcdf| 46;\n 24 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070fe227-b533-4c77-bed0-4d005b174920 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "GTN 'Pangeo 101 for everyone - Xarray'",
"outputs": [
{
@@ -85810,23 +75157,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json",
- "contributions": {
- "authorship": [
- "annefou",
- "huitang-earth"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "bernt-matthias",
- "beatrizserrano",
- "annefou",
- "bgruening",
- "natefoo",
- "martenson",
- "bebatut"
- ]
- },
"contributors": [
{
"elixir_node": "no",
@@ -85845,188 +75175,6 @@
"orcid": "0000-0002-8745-3859",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/huitang-earth/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/huitang-earth.json"
- },
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- "elixir-converge"
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- "elixir_node": "nl",
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- "avans-atgm",
- "uni-freiburg"
- ],
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- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
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- "email": "saskia.hiltemann@gmail.com",
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- "fediverse_flavor": "mastodon",
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- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "elixir_node": "de",
- "id": "bernt-matthias",
- "joined": "2017-09",
- "name": "Matthias Bernt",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
- },
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- "id": "beatrizserrano",
- "joined": "2020-07",
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- "matrix": "beatrizserrano:matrix.org",
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- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
- },
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- "name": "Anne Fouilloux",
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "martenson:matrix.org",
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}
],
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@@ -86063,7 +75211,7 @@
"Creating multi-case scenarios.",
"Composing, executing and publishing CML-FATES workflow."
],
- "pageviews": 6181159,
+ "pageviews": 6204138,
"pub_date": "2020-10-25",
"questions": [
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@@ -86105,12 +75253,12 @@
],
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+ "__EXTRACT_DATASET__",
"tp_find_and_replace",
"xarray_select",
- "xarray_metadata_info",
"ggplot2_point",
- "ctsm_fates",
- "__EXTRACT_DATASET__",
+ "xarray_metadata_info",
"interactive_tool_panoply"
],
"slides": true,
@@ -86165,6 +75313,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -86220,10 +75372,6 @@
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"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -86270,11 +75418,6 @@
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- "url": "https://usegalaxy.fr/",
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"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -86319,6 +75462,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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@@ -86371,10 +75518,6 @@
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@@ -86415,10 +75558,6 @@
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"state": "local"
@@ -86461,6 +75600,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -86513,10 +75656,6 @@
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@@ -86557,10 +75696,6 @@
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"state": "missing"
@@ -86603,6 +75738,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -86707,11 +75842,6 @@
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"state": "exact",
@@ -86757,6 +75887,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
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"state": "missing"
@@ -86903,6 +76029,10 @@
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@@ -86955,10 +76085,6 @@
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@@ -87001,14 +76127,6 @@
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{
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"state": "exact",
@@ -87054,6 +76172,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -87106,10 +76228,6 @@
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@@ -87152,14 +76270,6 @@
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{
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"state": "exact",
@@ -87205,6 +76315,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -87261,10 +76375,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -87313,11 +76423,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -87376,8 +76481,8 @@
"video": true,
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"video_view": 0,
- "visit_duration": 275,
- "visitors": 2243774,
+ "visit_duration": 274,
+ "visitors": 2254600,
"workflows": [
{
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@@ -87498,7 +76603,7 @@
],
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "CLM-FATES_ ALP1 simulation (5 years)",
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{
@@ -88211,7 +77316,7 @@
"Learn to get temperature variations.",
"Learn to use an interactive tool to visualise Argo temperature variable on an interactive map."
],
- "pageviews": 173,
+ "pageviews": 177,
"pub_date": "2024-03-24",
"questions": [
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@@ -88229,10 +77334,10 @@
"short_id": "T00428",
"short_tools": [
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+ "argo_getdata",
"interactive_tool_odv",
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- "argo_getdata"
+ "xarray_metadata_info",
+ "xarray_coords_info"
],
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"slides_recordings": false,
@@ -88268,6 +77373,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -88323,10 +77432,6 @@
"name": "InteractoMIX",
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -88373,11 +77478,6 @@
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"usegalaxy": true
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"url": "https://usegalaxy.no/",
@@ -88422,6 +77522,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -88474,10 +77578,6 @@
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@@ -88564,6 +77660,10 @@
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@@ -88662,9 +77758,145 @@
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- "version": "2022.3.0+galaxy0"
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"state": "missing"
@@ -88997,6 +78080,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -89049,10 +78136,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -89095,11 +78178,6 @@
"state": "exact",
"version": "2022.3.0+galaxy0"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.3.0+galaxy0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -89163,8 +78241,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 81,
- "visitors": 143,
+ "visit_duration": 78,
+ "visitors": 147,
"workflows": [
{
"creators": [
@@ -89195,7 +78273,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Argo data access\"];\n 1[\"NetCDF xarray Coordinate Info\"];\n 0 -->|output_argo| 1;\n 2[\"NetCDF xarray Metadata Info\"];\n 0 -->|output_argo| 2;\n 3[\"NetCDF timeseries Extractor\"];\n 0 -->|output_argo| 3;\n 2 -->|output| 3;\n 4[\"ODV\"];\n 3 -->|timeseries_tabular| 4;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Analyse Argo data ",
"outputs": [],
"parent_id": "climate/argo_pangeo",
@@ -89237,18 +78315,6 @@
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@@ -89259,110 +78325,6 @@
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"twitter": "AnneFouilloux",
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@@ -89413,7 +78375,7 @@
"Learn to resample my data",
"Learn to cite and contribute to Pangeo"
],
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"What is Pangeo notebook?",
@@ -89503,6 +78465,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -89558,10 +78524,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -89608,11 +78570,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -89657,6 +78614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -89709,10 +78670,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -89753,10 +78710,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
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{
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"state": "missing"
@@ -89808,7 +78761,7 @@
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"visit_duration": 273,
- "visitors": 1632741,
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@@ -89846,7 +78799,7 @@
"inputs": [],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"Pangeo Jupyter for Big Data geoscience\"];",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Pangeo Jupyter Notebook",
"outputs": [
{
@@ -89931,19 +78884,6 @@
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@@ -89961,112 +78901,6 @@
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@@ -90091,7 +78925,7 @@
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"mod_date": "2023-01-12",
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@@ -90163,7 +78997,7 @@
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"visit_duration": 153,
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+ "visitors": 2253323
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@@ -90174,20 +79008,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/panoply/tutorial.json",
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- "annefou",
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- "martenson"
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@@ -90198,161 +79018,6 @@
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"twitter": "AnneFouilloux",
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@@ -90382,7 +79047,7 @@
"Learn to use Panoply in Galaxy to visuallize netCDF geo-referenced data",
"Learn how Panoply plots are exported to Galaxy"
],
- "pageviews": 9686,
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"pub_date": "2020-03-05",
"questions": [
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@@ -90435,6 +79100,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -90490,10 +79159,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -90540,11 +79205,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
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],
"inexact": []
@@ -90965,6 +79615,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -91594,6 +80064,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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{
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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"state": "missing"
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],
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"short_tools": [
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"argo_getdata",
+ "spocc_occ",
"c3s",
"obis_data"
],
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"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"name": "InteractoMIX",
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{
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"url": "https://usegalaxy.eu",
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{
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "deNBI",
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- "elixir-converge",
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- "elixir-europe"
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- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
- "linkedin": "bgruening",
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
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- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "simonbray",
- "joined": "2019-05",
- "name": "Simon Bray",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "id": "chrisbarnettster",
- "joined": "2019-05",
- "name": "Christopher Barnett",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
}
],
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@@ -94238,7 +82553,7 @@
"Create a small compound library using the ChEMBL database",
"Dock a variety of ligands to the active site of the Hsp90 protein"
],
- "pageviews": 29263,
+ "pageviews": 29317,
"pub_date": "2019-10-19",
"questions": [
"What is cheminformatics?",
@@ -94247,30 +82562,30 @@
],
"short_id": "T00048",
"short_tools": [
- "ctb_online_data_fetch",
+ "ctb_filter",
+ "ctb_remIons",
+ "sdf_to_tab",
+ "chembl",
+ "prepare_receptor",
+ "ctb_change_title",
"tp_cat",
+ "ctb_np-likeness-calculator",
+ "ctb_remDuplicates",
+ "tp_grep_tool",
"ctb_chemfp_mol2fps",
+ "get_pdb",
+ "docking",
+ "ctb_online_data_fetch",
+ "openbabel_svg_depiction",
+ "ctb_compound_convert",
+ "prepare_box",
"ctb_chemfp_nxn_clustering",
"ctb_chemfp_butina_clustering",
+ "ctb_obgrep",
"openbabel_compound_convert",
- "ctb_compound_convert",
- "tp_grep_tool",
- "ctb_remIons",
- "prepare_receptor",
"collapse_dataset",
- "openbabel_svg_depiction",
- "ctb_np-likeness-calculator",
- "sdf_to_tab",
- "docking",
- "tp_find_and_replace",
- "get_pdb",
- "chembl",
"fpocket",
- "ctb_obgrep",
- "prepare_box",
- "ctb_change_title",
- "ctb_filter",
- "ctb_remDuplicates"
+ "tp_find_and_replace"
],
"slides": false,
"slides_recordings": false,
@@ -94306,6 +82621,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -94361,10 +82680,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -94411,11 +82726,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -94460,6 +82770,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -94512,10 +82826,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -94560,10 +82870,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -94613,6 +82919,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -94665,10 +82975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -94713,10 +83019,6 @@
"state": "exact",
"version": "2021.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -94766,6 +83068,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -94818,10 +83124,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -94864,10 +83166,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -94913,6 +83211,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -94965,10 +83267,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95011,10 +83309,6 @@
"state": "exact",
"version": "0.10.1+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -95060,6 +83354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95112,10 +83410,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95161,10 +83455,6 @@
"state": "exact",
"version": "1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -95214,6 +83504,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95266,10 +83560,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95318,10 +83608,6 @@
"0.3.0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -95375,6 +83661,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95427,10 +83717,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95476,10 +83762,6 @@
"state": "exact",
"version": "1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -95529,6 +83811,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95581,10 +83867,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95632,17 +83914,13 @@
"state": "exact",
"version": "0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.5.1",
- "1.6",
- "1.6.1+0"
+ "1.6.1+0",
+ "1.6"
]
},
{
@@ -95689,6 +83967,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95741,10 +84023,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95790,10 +84068,6 @@
"state": "exact",
"version": "1.5.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -95843,6 +84117,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -95895,10 +84173,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -95942,10 +84216,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -95991,6 +84261,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96043,10 +84317,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96091,10 +84361,6 @@
"state": "exact",
"version": "3.1.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -96144,6 +84410,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96197,10 +84467,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96244,10 +84510,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -96293,6 +84555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96345,10 +84611,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96391,10 +84653,6 @@
"state": "exact",
"version": "2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -96440,6 +84698,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96492,10 +84754,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96536,10 +84794,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -96583,6 +84837,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96635,10 +84893,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96679,10 +84933,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -96726,6 +84976,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96778,10 +85032,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96822,10 +85072,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -96869,6 +85115,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -96921,10 +85171,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -96965,10 +85211,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
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@@ -97155,6 +85393,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -97299,6 +85533,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -97450,6 +85680,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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+ "state": "missing"
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@@ -97900,6 +86117,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -97954,10 +86175,6 @@
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@@ -98054,6 +86266,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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"state": "exact",
@@ -98208,6 +86415,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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@@ -98317,14 +86524,6 @@
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{
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@@ -98400,7 +86599,7 @@
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"video_view": 0,
"visit_duration": 92,
- "visitors": 16578,
+ "visitors": 16625,
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@@ -98459,7 +86658,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 11[\"Compound Search\"];\n 5 -->|outfile| 11;\n 13[\"Remove duplicated molecules\"];\n 5 -->|outfile| 13;\n 19[\"Remove counterions and fragments\"];\n 13 -->|outfile| 19;\n 2[\"Online data\"];\n 29[\"Filter\"];\n 19 -->|outfile| 29;\n 30[\"Compound Convert\"];\n 19 -->|outfile| 30;\n 31[\"Molecules to Fingerprints\"];\n 19 -->|outfile| 31;\n 39[\"Natural Product\"];\n 29 -->|outfile| 39;\n 40[\"Molecules to Fingerprints\"];\n 29 -->|outfile| 40;\n 44[\"NxN Clustering\"];\n 40 -->|outfile| 44;\n 5[\"Change Title\"];\n 2 -->|output| 5;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "CTB Workflow",
"outputs": [],
"parent_id": "computational-chemistry/cheminformatics",
@@ -98618,17 +86817,6 @@
},
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- "reviewing": [
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@@ -98641,111 +86829,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
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- "elixir-europe"
- ],
- "id": "simonbray",
- "joined": "2019-05",
- "name": "Simon Bray",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/computational-chemistry/tutorials/covid19-docking",
@@ -98774,7 +86857,7 @@
"Replicate the study on a (very) small scale",
"Gain familiarity with the docking and scoring techniques involved."
],
- "pageviews": 4641,
+ "pageviews": 4647,
"pub_date": "2020-03-27",
"questions": [
"How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -98793,17 +86876,17 @@
"short_id": "T00049",
"short_tools": [
"sucos_max_score",
- "rdock_rbdock",
- "rxdock_rbcavity",
+ "collapse_dataset",
"openbabel_compound_convert",
- "rxdock_rbdock",
+ "rdock_rbcavity",
"xchem_pose_scoring",
- "split_file_to_collection",
- "enumerate_charges",
"xchem_transfs_scoring",
- "rdock_rbcavity",
+ "rxdock_rbdock",
+ "split_file_to_collection",
+ "rxdock_rbcavity",
"ctb_frankenstein_ligand",
- "collapse_dataset"
+ "rdock_rbdock",
+ "enumerate_charges"
],
"slides": false,
"slides_recordings": false,
@@ -98833,6 +86916,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -98888,10 +86975,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -98938,11 +87021,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -98987,6 +87065,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99039,10 +87121,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99088,10 +87166,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -99141,6 +87215,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99193,10 +87271,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99242,10 +87316,6 @@
"state": "exact",
"version": "2013.1-0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -99291,6 +87361,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99343,10 +87417,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99392,10 +87462,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -99445,6 +87511,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99497,10 +87567,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99546,10 +87612,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -99595,6 +87657,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99650,10 +87716,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99699,10 +87761,6 @@
"state": "exact",
"version": "2.4.2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -99750,6 +87808,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99803,10 +87865,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -99852,10 +87910,6 @@
"state": "exact",
"version": "3.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -99901,6 +87955,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -99953,10 +88011,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -100002,10 +88056,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -100054,6 +88104,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100106,10 +88160,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -100153,10 +88203,6 @@
"state": "exact",
"version": "0.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -100205,6 +88251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100257,10 +88307,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -100303,10 +88349,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -100356,6 +88398,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100408,10 +88454,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -100454,10 +88496,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -100507,6 +88545,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100560,10 +88602,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -100611,11 +88649,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -100661,6 +88694,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100693,8 +88730,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.4.0",
- "0.5.1"
+ "0.5.1",
+ "0.4.0"
]
},
{
@@ -100717,10 +88754,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -100771,11 +88804,6 @@
"state": "exact",
"version": "0.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -100821,6 +88849,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -100873,10 +88905,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -100922,10 +88950,6 @@
"state": "exact",
"version": "0.2.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -100975,6 +88999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -101027,10 +89055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -101076,10 +89100,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -101125,6 +89145,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -101177,10 +89201,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -101224,10 +89244,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -101272,6 +89288,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -101328,10 +89348,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -101381,14 +89397,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -101434,6 +89442,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -101486,10 +89498,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -101530,10 +89538,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -101600,8 +89604,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 177,
- "visitors": 2771,
+ "visit_duration": 179,
+ "visitors": 2777,
"workflows": [
{
"creators": [],
@@ -101743,7 +89747,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Enumerate changes\"];\n 0 -->|output| 3;\n 4[\"Compound conversion\"];\n 1 -->|output| 4;\n 5[\"Create Frankenstein ligand\"];\n 2 -->|output| 5;\n 6[\"Compound conversion\"];\n 3 -->|output| 6;\n 7[\"rDock cavity definition\"];\n 4 -->|outfile| 7;\n 5 -->|outfile| 7;\n 8[\"Split file\"];\n 6 -->|outfile| 8;\n 9[\"rDock docking\"];\n 4 -->|outfile| 9;\n 8 -->|list_output_sdf| 9;\n 7 -->|activesite| 9;\n 10[\"Collapse Collection\"];\n 9 -->|output| 10;\n 11[\"XChem TransFS pose scoring\"];\n 1 -->|output| 11;\n 10 -->|output| 11;\n 12[\"Max SuCOS score\"];\n 11 -->|output| 12;\n 2 -->|output| 12;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
"outputs": [
{
@@ -102144,7 +90148,7 @@
"Explore the databases used for drug discovery and development",
"Use Galaxy tools for data management, format conversion and simple analyses"
],
- "pageviews": 269,
+ "pageviews": 277,
"pub_date": "2024-01-08",
"questions": [
"Why does medicinal chemistry research produce so much data?",
@@ -102174,12 +90178,12 @@
],
"short_id": "T00381",
"short_tools": [
+ "openbabel_svg_depiction",
+ "openbabel_compound_convert",
"ctb_im_rxn_maker",
+ "md_converter",
"ctb_silicos_qed",
- "openbabel_compound_convert",
- "openbabel_svg_depiction",
"get_pdb",
- "md_converter",
"chembl"
],
"slides": false,
@@ -102237,6 +90241,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -102292,10 +90300,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -102342,11 +90346,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -102391,6 +90390,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -102443,10 +90446,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -102489,10 +90488,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -102538,6 +90533,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -102590,10 +90589,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -102636,10 +90631,6 @@
"state": "exact",
"version": "1.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -102685,6 +90676,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -102738,10 +90733,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -102785,10 +90776,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -102834,6 +90821,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -102887,10 +90878,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -102936,10 +90923,6 @@
"state": "exact",
"version": "3.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -102985,6 +90968,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -103037,10 +91024,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -103083,10 +91066,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -103132,6 +91111,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -103184,10 +91167,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -103230,10 +91209,6 @@
"state": "exact",
"version": "2021.03.4+galaxy0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -103279,6 +91254,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -103331,10 +91310,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -103380,10 +91355,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -103447,8 +91418,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 153,
- "visitors": 221,
+ "visit_duration": 149,
+ "visitors": 228,
"workflows": [
{
"creators": [
@@ -103533,7 +91504,7 @@
],
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Data management in Medicinal Chemistry workflow",
"outputs": [
{
@@ -103968,18 +91939,6 @@
},
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- "reviewing": [
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- "aurelienmoumbock",
- "hexylena",
- "shiltemann"
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"contributors": [
{
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@@ -104002,90 +91961,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
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- "elixir-europe",
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- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
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- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "linkedin": "shiltemann",
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}
],
"dir": "topics/computational-chemistry/tutorials/zauberkugel",
@@ -104118,7 +91993,7 @@
"Screen the query ligand against a pharmacophore library.",
"Analyze the results of the protein target prediction."
],
- "pageviews": 1515,
+ "pageviews": 1516,
"pub_date": "2022-02-15",
"questions": [
"What is a pharmacophore model?",
@@ -104126,12 +92001,12 @@
],
"short_id": "T00054",
"short_tools": [
+ "rdconf",
+ "ctb_alignit",
+ "sort1",
"tp_cat",
"split_file_to_collection",
- "sort1",
- "ctb_alignit",
- "openbabel_addh",
- "rdconf"
+ "openbabel_addh"
],
"slides": false,
"slides_recordings": false,
@@ -104177,6 +92052,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -104232,10 +92111,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -104282,11 +92157,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -104331,6 +92201,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -104383,10 +92257,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -104427,10 +92297,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
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- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -104473,6 +92339,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -104526,153 +92396,145 @@
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+ "server": "https://mississippi.sorbonne-universite.fr",
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"Learn which analysis tools are available.",
"Analyse a protein and discuss the meaning behind each analysis."
],
- "pageviews": 54952,
+ "pageviews": 55025,
"pub_date": "2019-06-03",
"questions": [
"Which analysis tools are available?"
@@ -107369,14 +94873,14 @@
],
"short_id": "T00047",
"short_tools": [
- "bio3d_pca",
- "mdanalysis_cosine_analysis",
+ "mdanalysis_rdf",
+ "bio3d_rmsd",
"mdanalysis_distance",
"mdanalysis_ramachandran_plot",
- "bio3d_rmsd",
+ "bio3d_pca",
+ "mdanalysis_dihedral",
"bio3d_rmsf",
- "mdanalysis_rdf",
- "mdanalysis_dihedral"
+ "mdanalysis_cosine_analysis"
],
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"slides_recordings": false,
@@ -107438,6 +94942,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://usegalaxy.no/",
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"visit_duration": 75,
- "visitors": 30297,
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@@ -109416,7 +96871,7 @@
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Analysis using MDAnalysis",
"outputs": [
{
@@ -109985,7 +97440,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Simple Analysis",
"outputs": [
{
@@ -110417,25 +97872,6 @@
},
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- "stephanierobin",
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@@ -110493,149 +97929,6 @@
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@@ -110672,7 +97965,7 @@
"Learn how to conduct MD simulation and analysis for a protein-ligand system",
"Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein."
],
- "pageviews": 16370,
+ "pageviews": 16424,
"pub_date": "2020-05-20",
"questions": [
"How are protein-ligand systems parameterized for molecular dynamics simulation?",
@@ -110696,24 +97989,24 @@
],
"short_id": "T00050",
"short_tools": [
- "gmx_solvate",
- "gmx_setup",
+ "bio3d_rmsf",
+ "vmd_hbonds",
"openbabel_compound_convert",
- "ambertools_acpype",
+ "bio3d_rmsd",
"bio3d_pca_visualize",
+ "gmx_em",
+ "gmx_solvate",
+ "gmx_setup",
+ "md_converter",
"gmx_merge_topology_files",
"bio3d_pca",
- "get_pdb",
- "md_converter",
- "mdanalysis_cosine_analysis",
+ "gmx_sim",
"tp_grep_tool",
- "bio3d_rmsd",
- "gmx_editconf",
- "bio3d_rmsf",
+ "ambertools_acpype",
"gmx_energy",
- "gmx_sim",
- "gmx_em",
- "vmd_hbonds"
+ "gmx_editconf",
+ "mdanalysis_cosine_analysis",
+ "get_pdb"
],
"slides": false,
"slides_recordings": false,
@@ -110770,6 +98063,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "http://galaxy.interactomix.com/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -110875,11 +98168,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -110924,6 +98212,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -110977,10 +98269,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -111024,10 +98312,6 @@
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{
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"state": "exact",
@@ -111073,6 +98357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -111128,10 +98416,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -111177,10 +98461,6 @@
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{
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"state": "inexact",
@@ -111228,6 +98508,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -111281,10 +98565,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -111330,10 +98610,6 @@
"state": "exact",
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},
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -111379,6 +98655,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -111433,10 +98713,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -111483,11 +98759,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -111533,6 +98804,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -111588,10 +98863,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -111637,10 +98908,6 @@
"state": "exact",
"version": "19.11"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -111686,6 +98953,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -111741,10 +99012,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -111792,10 +99059,6 @@
"state": "exact",
"version": "21.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -111843,6 +99106,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -111896,10 +99163,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -111943,10 +99206,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -111992,6 +99251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112045,10 +99308,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112092,10 +99351,6 @@
"state": "exact",
"version": "2.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -112141,6 +99396,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112194,10 +99453,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112241,10 +99496,6 @@
"state": "exact",
"version": "2.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -112290,6 +99541,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112343,10 +99598,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112390,10 +99641,6 @@
"state": "exact",
"version": "2.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -112439,6 +99686,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112494,10 +99745,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112548,10 +99795,6 @@
"2020.4+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -112599,6 +99842,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112654,10 +99901,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112706,10 +99949,6 @@
"state": "exact",
"version": "2020.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -112757,6 +99996,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112812,10 +100055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -112868,10 +100107,6 @@
"2021.3+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -112919,6 +100154,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -112974,10 +100213,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113010,8 +100245,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2019.1.4",
- "2020.2+galaxy0"
+ "2020.2+galaxy0",
+ "2019.1.4"
]
},
{
@@ -113026,10 +100261,6 @@
"state": "exact",
"version": "2020.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -113077,6 +100308,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113132,10 +100367,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113180,10 +100411,6 @@
"state": "exact",
"version": "2020.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -113231,6 +100458,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113286,10 +100517,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113335,10 +100562,6 @@
"state": "exact",
"version": "3.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -113386,6 +100609,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113441,10 +100668,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113492,10 +100715,6 @@
"state": "exact",
"version": "3.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -113541,6 +100760,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113596,10 +100819,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113645,10 +100864,6 @@
"state": "exact",
"version": "2019.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -113696,6 +100911,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113751,10 +100970,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113803,10 +101018,6 @@
"state": "exact",
"version": "2020.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -113854,6 +101065,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -113909,10 +101124,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -113966,10 +101177,6 @@
"2020.4+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114017,6 +101224,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114072,10 +101283,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114124,10 +101331,6 @@
"state": "exact",
"version": "2020.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114175,6 +101378,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114230,10 +101437,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114282,15 +101485,11 @@
"2020.2+galaxy0",
"2022+galaxy0",
"2021.3+galaxy0",
+ "2020.2+galaxy1",
"2020.4+galaxy1",
- "2020.4+galaxy0",
- "2020.2+galaxy1"
+ "2020.4+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114338,6 +101537,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114393,10 +101596,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114445,10 +101644,6 @@
"state": "exact",
"version": "2020.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114496,6 +101691,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114548,10 +101747,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114597,10 +101792,6 @@
"state": "exact",
"version": "1.9.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -114646,6 +101837,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114698,10 +101893,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114747,10 +101938,6 @@
"state": "exact",
"version": "1.9.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114798,6 +101985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -114853,10 +102044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -114902,10 +102089,6 @@
"state": "exact",
"version": "0.20"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -114953,6 +102136,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -115006,10 +102193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -115055,10 +102238,6 @@
"state": "exact",
"version": "1.0.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -115104,6 +102283,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -115156,10 +102339,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -115203,10 +102382,6 @@
"state": "exact",
"version": "1.9.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -115283,8 +102458,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 157,
- "visitors": 8903,
+ "visit_duration": 156,
+ "visitors": 8946,
"workflows": [
{
"creators": [],
@@ -115368,7 +102543,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"GROMACS structure configuration\"];\n 0 -->|output| 2;\n 3[\"MDTraj file converter\"];\n 1 -->|output| 3;\n 4[\"RMSD Analysis\"];\n 2 -->|output| 4;\n 3 -->|output| 4;\n 5[\"RMSF Analysis\"];\n 2 -->|output| 5;\n 3 -->|output| 5;\n 6[\"PCA\"];\n 2 -->|output| 6;\n 3 -->|output| 6;\n 7[\"Cosine Content\"];\n 3 -->|output| 7;\n 2 -->|output| 7;\n 8[\"PCA visualization\"];\n 2 -->|output| 8;\n 3 -->|output| 8;\n 9[\"Hydrogen Bond Analysis using VMD\"];\n 3 -->|output| 9;\n 2 -->|output| 9;\n 10[\"RMSD Analysis\"];\n 2 -->|output| 10;\n 3 -->|output| 10;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Workflow constructed from history 'Hsp90-MDAnalysis'",
"outputs": [],
"parent_id": "computational-chemistry/htmd-analysis",
@@ -115484,7 +102659,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"Get PDB file\"];\n 0 -->|output| 2;\n 3[\"Search in textfiles\"];\n 2 -->|output| 3;\n 4[\"Search in textfiles\"];\n 2 -->|output| 4;\n 1 -->|output| 4;\n 5[\"GROMACS initial setup\"];\n 3 -->|output| 5;\n 6[\"Compound conversion\"];\n 4 -->|output| 6;\n 7[\"Generate MD topologies for small molecules\"];\n 6 -->|outfile| 7;\n 8[\"Merge GROMACS topologies\"];\n 7 -->|gro_output| 8;\n 5 -->|output1| 8;\n 5 -->|output2| 8;\n 7 -->|output| 8;\n 9[\"GROMACS structure configuration\"];\n 8 -->|complex_gro| 9;\n 10[\"GROMACS solvation and adding ions\"];\n 8 -->|complex_top| 10;\n 9 -->|output| 10;\n 11[\"GROMACS energy minimization\"];\n 10 -->|output2| 11;\n 10 -->|output1| 11;\n 12[\"GROMACS simulation\"];\n 5 -->|output3| 12;\n 10 -->|output2| 12;\n 11 -->|output1| 12;\n 13[\"GROMACS simulation\"];\n 5 -->|output3| 13;\n 10 -->|output2| 13;\n 12 -->|output1| 13;\n 12 -->|output5| 13;\n 14[\"GROMACS simulation\"];\n 10 -->|output2| 14;\n 13 -->|output1| 14;\n 13 -->|output5| 14;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "MD protein-ligand workflow (from PDB structure)",
"outputs": [
{
@@ -115672,21 +102847,6 @@
},
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- "hexylena",
- "bgruening",
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- "bebatut",
- "chrisbarnettster",
- "lecorguille",
- "cat-bro"
- ]
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"contributors": [
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"elixir_node": "de",
@@ -115699,167 +102859,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
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- "elixir-europe"
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- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir_node": "nl",
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- "avans-atgm",
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- "fediverse": "https://fosstodon.org/@bgruening",
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
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- "fediverse": "https://piaille.fr/@bebatut",
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- "linkedin": "berenicebatut",
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- },
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- "name": "Christopher Barnett",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "au",
- "id": "cat-bro",
- "joined": "2019-12",
- "matrix": "cat-bro:matrix.org",
- "name": "Catherine Bromhead",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cat-bro/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/cat-bro.json"
}
],
"dir": "topics/computational-chemistry/tutorials/md-simulation-gromacs",
@@ -115907,7 +102906,7 @@
"Understand the structure of the molecular dynamics workflow.",
"Prepare a short (1 ns) trajectory for a simulation of a protein."
],
- "pageviews": 44137,
+ "pageviews": 44201,
"pub_date": "2019-06-03",
"questions": [
"How do I use the GROMACS engine in Galaxy?",
@@ -115915,13 +102914,13 @@
],
"short_id": "T00051",
"short_tools": [
+ "gmx_em",
"gmx_solvate",
"gmx_setup",
- "get_pdb",
- "gmx_editconf",
- "tp_grep_tool",
"gmx_sim",
- "gmx_em"
+ "tp_grep_tool",
+ "get_pdb",
+ "gmx_editconf"
],
"slides": false,
"slides_recordings": false,
@@ -115988,6 +102987,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -116043,10 +103046,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -116093,11 +103092,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -116142,6 +103136,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116195,10 +103193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -116242,10 +103236,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -116291,6 +103281,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116345,10 +103339,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -116395,11 +103385,6 @@
"state": "exact",
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},
- {
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- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -116445,6 +103430,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116500,10 +103489,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -116549,10 +103534,6 @@
"state": "exact",
"version": "2020.2+galaxy0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -116598,6 +103579,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116653,10 +103638,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -116705,10 +103686,6 @@
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},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -116756,6 +103733,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116811,10 +103792,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -116860,10 +103837,6 @@
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -116909,6 +103882,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -116964,10 +103941,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -117000,8 +103973,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2019.1.4",
- "2020.2+galaxy0"
+ "2020.2+galaxy0",
+ "2019.1.4"
]
},
{
@@ -117016,10 +103989,6 @@
"state": "exact",
"version": "2020.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -117067,6 +104036,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -117122,10 +104095,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -117171,10 +104140,6 @@
"state": "exact",
"version": "2020.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -117220,6 +104185,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -117275,10 +104244,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
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@@ -117327,10 +104292,6 @@
"state": "exact",
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},
- {
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- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -117378,6 +104339,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -117433,10 +104398,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
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- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "affiliations": [
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- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
- "id": "martenson",
- "joined": "2017-09",
- "location": {
- "country": "USA",
- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/contributing/tutorials/running-jekyll",
@@ -123764,7 +108777,7 @@
"Running the GTN material website locally",
"Tracking changes to the content live in the webbrowser"
],
- "pageviews": 1589,
+ "pageviews": 1594,
"priority": 2,
"pub_date": "2017-06-25",
"questions": [
@@ -123801,7 +108814,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 216,
- "visitors": 1154
+ "visitors": 1158
},
{
"admin_install": {
@@ -123883,28 +108896,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: ddf54b12c295\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: c3s\n owner: climate\n revisions: 250554670f72\n tool_panel_section_label: Climate Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bam_to_sam\n owner: devteam\n revisions: 88eedb4abea0\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n owner: devteam\n revisions: 017aba02828d\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_to_tabular\n owner: devteam\n revisions: 614a63f14adf\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n owner: iuc\n revisions: 3da72230c066\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 49370cb85f0f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial/tutorial.json",
- "contributions": {
- "authorship": [
- "bebatut",
- "hexylena",
- "shiltemann",
- "lldelisle"
- ],
- "reviewing": [
- "hexylena",
- "bebatut",
- "shiltemann",
- "nsoranzo",
- "bgruening",
- "yvanlebras",
- "lecorguille",
- "simonbray",
- "wm75",
- "slugger70",
- "abretaud",
- "njall"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -124012,255 +109003,16 @@
"orcid": "0000-0002-1964-4960",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
- },
- {
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
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- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe"
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- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
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- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "gallantries",
- "fairease",
- "fnso2019",
- "elixir-europe"
- ],
- "elixir_node": "fr",
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- "id": "yvanlebras",
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- "name": "Yvan Le Bras",
- "orcid": "0000-0002-8504-068X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
- "twitter": "Yvan2935",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
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- },
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- "elixir-europe"
- ],
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- },
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- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "elixir_node": "au",
- "email": "simon.gladman@unimelb.edu.au",
- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
- "orcid": "0000-0002-6100-4385",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/contributing/tutorials/create-new-tutorial",
"edam_operation": [
+ "Sequence file editing",
"Data handling",
- "Read mapping",
- "Read pre-processing",
"Sequence trimming",
"Primer removal",
- "Sequence file editing"
+ "Read mapping",
+ "Read pre-processing"
],
"edam_topic": [],
"feedback_mean_note": null,
@@ -124284,7 +109036,7 @@
"Create hands-on",
"Add technical support for a tutorial"
],
- "pageviews": 2225,
+ "pageviews": 2229,
"priority": 3,
"pub_date": "2018-06-20",
"questions": [
@@ -124307,19 +109059,19 @@
],
"short_id": "T00057",
"short_tools": [
- "c3s",
- "tp_cut_tool",
- "bowtie2",
+ "tp_sed_tool",
+ "Filter1",
+ "Cut1",
"tp_cat",
"cutadapt",
- "random_lines1",
- "Filter1",
- "bam_to_sam",
"fastq_to_tabular",
- "tp_sorted_uniq",
+ "random_lines1",
"seqtk_subseq",
- "tp_sed_tool",
- "Cut1"
+ "tp_cut_tool",
+ "c3s",
+ "bowtie2",
+ "tp_sorted_uniq",
+ "bam_to_sam"
],
"slides": false,
"slides_recordings": false,
@@ -124363,8 +109115,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 313,
- "visitors": 1473,
+ "visit_duration": 312,
+ "visitors": 1477,
"workflows": [
{
"creators": [],
@@ -124462,7 +109214,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSRR891268_R1_20M.fastq.gz\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSRR891268_R2_20M.fastq.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Unique\"];\n 9 -->|out_file1| 10;\n 11[\"Text transformation\"];\n 10 -->|outfile| 11;\n 12[\"Concatenate datasets\"];\n 6 -->|out_file1| 12;\n 11 -->|output| 12;\n 13[\"Unique\"];\n 12 -->|out_file1| 13;\n 14[\"seqtk_subseq\"];\n 0 -->|output| 14;\n 13 -->|outfile| 14;\n 15[\"Text transformation\"];\n 13 -->|outfile| 15;\n 16[\"seqtk_subseq\"];\n 1 -->|output| 16;\n 15 -->|output| 16;\n 2[\"FASTQ to Tabular\"];\n 0 -->|output| 2;\n 3[\"Cutadapt\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Cut\"];\n 2 -->|output_file| 4;\n 5[\"Bowtie2\"];\n 3 -->|out1| 5;\n 3 -->|out2| 5;\n 6[\"Select random lines\"];\n 4 -->|output| 6;\n 7[\"BAM-to-SAM\"];\n 5 -->|output| 7;\n 8[\"Filter\"];\n 7 -->|output1| 8;\n 9[\"Cut\"];\n 8 -->|out_file1| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "MakeAFakeInput",
"outputs": [],
"parent_id": "contributing/create-new-tutorial",
@@ -124559,7 +109311,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAPI Request file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Copernicus Climate Data Store\"];\n 0 -->|output| 1;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Retrieve climate data from Copernicus",
"outputs": [
{
@@ -124755,7 +109507,7 @@
"language": "r"
},
"objectives": null,
- "pageviews": 7,
+ "pageviews": 8,
"priority": 3,
"pub_date": "2024-11-07",
"questions": null,
@@ -124802,7 +109554,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 0,
- "visitors": 7
+ "visitors": 8
},
{
"abbreviations": {
@@ -124914,14 +109666,14 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Learn about metadata and findability",
"Learn how to support system and content curation"
],
"pageviews": 0,
"priority": 3,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
"What are the FAIR training materials?",
"How to test, reproduce and share your content?",
@@ -125649,8 +110401,8 @@
],
"dir": "topics/contributing/tutorials/create-new-tutorial-content",
"edam_operation": [
- "Validation",
- "Sequencing quality control"
+ "Sequencing quality control",
+ "Validation"
],
"edam_topic": [],
"feedback_mean_note": null,
@@ -125672,7 +110424,7 @@
"Create hands-on",
"Use the different boxes"
],
- "pageviews": 9272,
+ "pageviews": 9281,
"priority": 4,
"pub_date": "2017-06-25",
"questions": [
@@ -125717,7 +110469,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 124,
- "visitors": 3361
+ "visitors": 3368
},
{
"admin_install": {
@@ -125728,23 +110480,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-slides/tutorial.json",
- "contributions": {
- "authorship": [
- "hexylena",
- "bebatut",
- "shiltemann"
- ],
- "reviewing": [
- "hexylena",
- "nsoranzo",
- "shiltemann",
- "bgruening",
- "gallardoalba",
- "martenson",
- "bebatut",
- "njall"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -125833,185 +110568,6 @@
"orcid": "0000-0003-3803-468X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
- "id": "martenson",
- "joined": "2017-09",
- "location": {
- "country": "USA",
- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/contributing/tutorials/create-new-tutorial-slides",
@@ -126037,7 +110593,7 @@
"Create a new set of slides",
"Add presenter comments"
],
- "pageviews": 6179067,
+ "pageviews": 6202042,
"priority": 5,
"pub_date": "2018-06-13",
"questions": [
@@ -126104,7 +110660,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 153,
- "visitors": 2242499
+ "visitors": 2253323
},
{
"admin_install": {
@@ -126249,7 +110805,7 @@
"objectives": [
"Implement tutorial tool version update on existing GTN material"
],
- "pageviews": 1,
+ "pageviews": 2,
"priority": 6,
"pub_date": "2024-11-29",
"questions": [
@@ -126296,7 +110852,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 0,
- "visitors": 1
+ "visitors": 2
},
{
"admin_install": {
@@ -126343,18 +110899,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bcftools_consensus\n owner: iuc\n revisions: e522022137f6\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n owner: iuc\n revisions: e188c9826e0f\n tool_panel_section_label: Expression Tools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n owner: iuc\n revisions: b6abccb1f25b\n tool_panel_section_label: Phylogenetics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n owner: iuc\n revisions: 5fab4f81391d\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 830961c48e42\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
- "contributions": {
- "authorship": [
- "simonbray",
- "wm75"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "wm75",
- "bebatut"
- ]
- },
"contributors": [
{
"elixir_node": "de",
@@ -126384,117 +110928,12 @@
"orcid": "0000-0002-9464-6640",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "by-covid",
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
}
],
"dir": "topics/galaxy-interface/tutorials/workflow-automation",
"edam_operation": [
- "Variant classification",
- "Tree-based sequence alignment"
+ "Tree-based sequence alignment",
+ "Variant classification"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -126508,8 +110947,7 @@
"hands_on": true,
"id": "galaxy-interface/workflow-automation",
"inexact_supported_servers": [
- "MISSISSIPPI",
- "UseGalaxy.fr"
+ "MISSISSIPPI"
],
"js_requirements": {
"mathjax": null,
@@ -126527,7 +110965,7 @@
"Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
"Learn how to use Pangolin to assign annotated variants to lineages."
],
- "pageviews": 2948,
+ "pageviews": 2952,
"pub_date": "2021-06-08",
"questions": [
"How can I schedule and run tens or hundreds of Galaxy workflows easily?",
@@ -126559,11 +110997,11 @@
],
"short_id": "T00162",
"short_tools": [
+ "snpSift_filter",
+ "collapse_dataset",
"bcftools_consensus",
"pangolin",
- "compose_text_param",
- "snpSift_filter",
- "collapse_dataset"
+ "compose_text_param"
],
"slides": false,
"slides_recordings": false,
@@ -126596,11 +111034,6 @@
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -126626,6 +111059,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -126681,10 +111118,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -126731,11 +111164,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -126780,6 +111208,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -126838,10 +111270,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -126891,11 +111319,6 @@
"state": "exact",
"version": "1.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.10"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -126941,6 +111364,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -126993,10 +111420,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -127040,11 +111463,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -127089,6 +111507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -127121,11 +111543,11 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
"3.0.3+galaxy0",
+ "4.1.1+galaxy0",
"4.0.5+galaxy0",
- "4.1.1+galaxy0"
+ "3.1.16+galaxy0",
+ "4.1.2+galaxy0"
]
},
{
@@ -127148,10 +111570,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -127201,26 +111619,6 @@
"state": "exact",
"version": "2.3.8"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
- "4.0.5+galaxy0",
- "4.1.1+galaxy0",
- "4.3+galaxy2",
- "4.2+galaxy0",
- "4.3+galaxy1",
- "3.1.17+galaxy1",
- "3.1.19+galaxy0",
- "3.1.20+galaxy0",
- "3.1.11+galaxy0",
- "4.0.5+galaxy2",
- "3.1.4+galaxy1",
- "3.1.14+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -127265,6 +111663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -127321,10 +111723,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -127369,11 +111767,6 @@
"state": "exact",
"version": "4.3+t.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -127419,6 +111812,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -127475,10 +111872,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -127528,14 +111921,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -127595,7 +111980,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 126,
- "visitors": 2392,
+ "visitors": 2396,
"workflows": [
{
"creators": [
@@ -127728,7 +112113,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Compose text parameter value\"];\n 1 -->|output| 3;\n 4[\"SnpSift Filter\"];\n 3 -->|out1| 4;\n 0 -->|output| 4;\n ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n 4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n 5[\"bcftools consensus\"];\n 4 -->|output| 5;\n 2 -->|output| 5;\n 9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n 5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n 6[\"Collapse Collection\"];\n 5 -->|output_file| 6;\n 1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n 6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n 7[\"Pangolin\"];\n 6 -->|output| 7;\n e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n 7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "vcf2lineage",
"outputs": [
{
@@ -128064,6 +112449,13 @@
"install_resolver_dependencies": true,
"install_tool_dependencies": true,
"tools": [
+ {
+ "name": "ena_webin_cli",
+ "owner": "ieguinoa",
+ "revisions": "7d751b5943b0",
+ "tool_panel_section_label": "Using Galaxy and Managing your Data",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "ena_upload",
"owner": "iuc",
@@ -128073,22 +112465,8 @@
}
]
},
- "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ena_upload\n owner: iuc\n revisions: 9e2df763086c\n tool_panel_section_label: Send Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+ "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ena_webin_cli\n owner: ieguinoa\n revisions: 7d751b5943b0\n tool_panel_section_label: Using Galaxy and Managing your Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ena_upload\n owner: iuc\n revisions: 9e2df763086c\n tool_panel_section_label: Send Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json",
- "contributions": {
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- "roncoronimiguel",
- "bedroesb",
- "B0r1sD"
- ],
- "reviewing": [
- "bedroesb",
- "hexylena",
- "shiltemann",
- "bgruening",
- "beatrizserrano"
- ]
- },
"contributors": [
{
"email": "miguel.roncoroni@elixir-belgium.org",
@@ -128130,125 +112508,6 @@
"name": "Boris Depoortere",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/B0r1sD/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/B0r1sD.json"
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- "elixir_node": "be",
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- "id": "bedroesb",
- "joined": "2019-12",
- "matrix": "bedroesb:matrix.org",
- "name": "Bert Droesbeke",
- "orcid": "0000-0003-0522-5674",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bedroesb/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bedroesb.json"
- },
- {
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
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- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
}
],
"dir": "topics/galaxy-interface/tutorials/upload-data-to-ena",
@@ -128259,7 +112518,9 @@
"feedback_number": 0,
"hands_on": true,
"id": "galaxy-interface/upload-data-to-ena",
- "inexact_supported_servers": [],
+ "inexact_supported_servers": [
+ "UseGalaxy.be"
+ ],
"js_requirements": {
"mathjax": null,
"mermaid": false
@@ -128274,12 +112535,12 @@
"layout": "tutorial_hands_on",
"level": "Intermediate",
"license": "CC-BY-4.0",
- "mod_date": "2024-04-04",
+ "mod_date": "2024-12-11",
"objectives": [
"Submit raw sequencing reads and metadata to ENA's test server",
"Submit consensus sequence and metadata to ENA's test server"
],
- "pageviews": 5088279,
+ "pageviews": 5111262,
"pub_date": "2021-08-10",
"questions": [
"How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -128303,13 +112564,19 @@
"short_id": "T00159",
"short_tools": [
"ena_upload",
- "ena_webin_cli"
+ "ena_consensus_submit"
],
"slides": true,
"slides_recordings": false,
"supported_servers": {
"exact": [],
- "inexact": []
+ "inexact": [
+ {
+ "name": "UseGalaxy.be",
+ "url": "https://usegalaxy.be/",
+ "usegalaxy": false
+ }
+ ]
},
"supported_servers_matrix": {
"servers": [
@@ -128333,6 +112600,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -128388,10 +112659,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -128438,11 +112705,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -128465,7 +112727,7 @@
],
"tools": [
{
- "id": "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_webin_cli/7d751b5943b0",
+ "id": "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_consensus_submit/4.3.0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -128487,6 +112749,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -128539,10 +112805,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -128573,7 +112835,8 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "missing"
+ "state": "exact",
+ "version": "4.3.0"
},
{
"server": "https://usegalaxy.cz/",
@@ -128583,10 +112846,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -128604,7 +112863,7 @@
"state": "missing"
}
],
- "version": "7d751b5943b0"
+ "version": "4.3.0"
},
{
"id": "toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2",
@@ -128629,6 +112888,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -128681,10 +112944,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -128720,9 +112979,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1"
]
},
@@ -128738,23 +112997,6 @@
"state": "exact",
"version": "0.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.7.3+galaxy1",
- "0.5.3",
- "0.3.1",
- "0.7.1+galaxy1",
- "0.6.1",
- "0.3.3",
- "0.6.3+galaxy0",
- "0.4.3",
- "0.6.0",
- "0.4.1",
- "0.7.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -128771,8 +113013,8 @@
"0.5.3",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
+ "0.3.3",
"0.4.3",
"0.6.0"
]
@@ -128807,6 +113049,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -128859,10 +113105,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -128898,9 +113140,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1"
]
},
@@ -128916,34 +113158,17 @@
"state": "inexact",
"versions": [
"0.7.3+galaxy1",
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
- "0.3.2",
- "0.4.3",
- "0.6.0",
- "0.4.1"
- ]
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- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
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- "0.5.3",
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- "0.7.1+galaxy1",
- "0.6.1",
"0.3.3",
- "0.6.3+galaxy0",
"0.4.3",
"0.6.0",
- "0.4.1",
- "0.7.1+galaxy0"
+ "0.3.2",
+ "0.4.1"
]
},
{
@@ -128962,8 +113187,8 @@
"0.5.3",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
+ "0.3.3",
"0.4.3",
"0.6.0"
]
@@ -128984,7 +113209,7 @@
"time_estimation": "1h",
"title": "Submitting sequence data to ENA",
"tools": [
- "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_webin_cli/7d751b5943b0",
+ "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_consensus_submit/4.3.0",
"toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2",
"toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.7.1"
],
@@ -129003,12 +113228,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json"
},
- "version": 9,
+ "version": 10,
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 238,
- "visitors": 1918758,
+ "visit_duration": 237,
+ "visitors": 1928826,
"workflows": [
{
"creators": [],
@@ -129032,7 +113257,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"ENA Upload tool\"];\n 1[\"ENA Upload tool\"];",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN_ENA_upload_workflow",
"outputs": [
{
@@ -129264,17 +113489,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n owner: bgruening\n revisions: 8e214e52e461\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n owner: bgruening\n revisions: 7255688c77f3\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n owner: bgruening\n revisions: 2a868592ebcb\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n owner: bgruening\n revisions: 67ee76f0e497\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n owner: bgruening\n revisions: b59c91adeac1\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n owner: bgruening\n revisions: e2c36f62e22f\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n owner: bgruening\n revisions: 744a777e9f90\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n owner: bgruening\n revisions: a22969b08177\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n owner: bgruening\n revisions: 7fac8e7a12d5\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n owner: bgruening\n revisions: 6fe6b0e10ed6\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n owner: bgruening\n revisions: '0046692724f9'\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n owner: bgruening\n revisions: 6cbe2f30c2d7\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n owner: bgruening\n revisions: d4c67ced6abc\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n owner: bgruening\n revisions: 9b48456a96fe\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n owner: bgruening\n revisions: f6f9b47d02b6\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 830961c48e42\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
- "contributions": {
- "authorship": [
- "simonbray"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "simonbray",
- "bgruening"
- ]
- },
"contributors": [
{
"elixir_node": "de",
@@ -129287,111 +113501,6 @@
"name": "Simon Bray",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
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- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "simonbray",
- "joined": "2019-05",
- "name": "Simon Bray",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/computational-chemistry/tutorials/covid19-docking",
@@ -129420,7 +113529,7 @@
"Replicate the study on a (very) small scale",
"Gain familiarity with the docking and scoring techniques involved."
],
- "pageviews": 4641,
+ "pageviews": 4647,
"pub_date": "2020-03-27",
"questions": [
"How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -129439,17 +113548,17 @@
"short_id": "T00049",
"short_tools": [
"sucos_max_score",
- "rdock_rbdock",
- "rxdock_rbcavity",
+ "collapse_dataset",
"openbabel_compound_convert",
- "rxdock_rbdock",
+ "rdock_rbcavity",
"xchem_pose_scoring",
- "split_file_to_collection",
- "enumerate_charges",
"xchem_transfs_scoring",
- "rdock_rbcavity",
+ "rxdock_rbdock",
+ "split_file_to_collection",
+ "rxdock_rbcavity",
"ctb_frankenstein_ligand",
- "collapse_dataset"
+ "rdock_rbdock",
+ "enumerate_charges"
],
"slides": false,
"slides_recordings": false,
@@ -129479,6 +113588,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -129534,10 +113647,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -129584,11 +113693,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -129633,6 +113737,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -129685,10 +113793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -129734,10 +113838,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -129787,6 +113887,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -129839,10 +113943,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -129888,10 +113988,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -129937,6 +114033,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -129989,10 +114089,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130038,10 +114134,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -130091,6 +114183,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130143,10 +114239,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130192,10 +114284,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -130241,6 +114329,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130296,10 +114388,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130345,10 +114433,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -130396,6 +114480,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130449,10 +114537,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130498,10 +114582,6 @@
"state": "exact",
"version": "3.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -130547,6 +114627,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130599,10 +114683,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130648,10 +114728,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -130700,6 +114776,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130752,10 +114832,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130799,10 +114875,6 @@
"state": "exact",
"version": "0.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -130851,6 +114923,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -130903,10 +114979,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -130949,10 +115021,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131002,6 +115070,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131054,10 +115126,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -131100,10 +115168,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131153,6 +115217,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131206,10 +115274,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -131257,11 +115321,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131307,6 +115366,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131339,8 +115402,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.4.0",
- "0.5.1"
+ "0.5.1",
+ "0.4.0"
]
},
{
@@ -131363,10 +115426,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -131417,11 +115476,6 @@
"state": "exact",
"version": "0.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131467,6 +115521,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131519,10 +115577,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -131568,10 +115622,6 @@
"state": "exact",
"version": "0.2.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -131621,6 +115671,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131673,10 +115727,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -131722,10 +115772,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131771,6 +115817,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131823,10 +115873,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -131870,10 +115916,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -131918,6 +115960,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -131974,10 +116020,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -132027,14 +116069,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -132080,6 +116114,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -132132,10 +116170,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -132176,10 +116210,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -132246,8 +116276,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 177,
- "visitors": 2771,
+ "visit_duration": 179,
+ "visitors": 2777,
"workflows": [
{
"creators": [],
@@ -132389,7 +116419,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Enumerate changes\"];\n 0 -->|output| 3;\n 4[\"Compound conversion\"];\n 1 -->|output| 4;\n 5[\"Create Frankenstein ligand\"];\n 2 -->|output| 5;\n 6[\"Compound conversion\"];\n 3 -->|output| 6;\n 7[\"rDock cavity definition\"];\n 4 -->|outfile| 7;\n 5 -->|outfile| 7;\n 8[\"Split file\"];\n 6 -->|outfile| 8;\n 9[\"rDock docking\"];\n 4 -->|outfile| 9;\n 8 -->|list_output_sdf| 9;\n 7 -->|activesite| 9;\n 10[\"Collapse Collection\"];\n 9 -->|output| 10;\n 11[\"XChem TransFS pose scoring\"];\n 1 -->|output| 11;\n 10 -->|output| 11;\n 12[\"Max SuCOS score\"];\n 11 -->|output| 12;\n 2 -->|output| 12;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
"outputs": [
{
@@ -132686,18 +116716,6 @@
},
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- "wm75",
- "bgruening",
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@@ -132715,143 +116733,22 @@
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- "elixir-converge"
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- "elixir_node": "nl",
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- "avans-atgm",
- "uni-freiburg"
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- ],
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- "fediverse_flavor": "mastodon",
- "id": "wm75",
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- "uni-freiburg",
- "elixir-europe"
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- "email": "bjoern.gruening@gmail.com",
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- "fediverse_flavor": "mastodon",
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- "Data handling",
- "Sequencing quality control",
- "Genome assembly",
- "Pairwise sequence alignment",
- "Box-Whisker plot plotting",
"Validation",
+ "Pairwise sequence alignment",
+ "Genome assembly",
+ "Read mapping",
+ "Sequence assembly visualisation",
+ "Sequencing quality control",
"Sequence file editing",
+ "Data handling",
+ "Sequence contamination filtering",
"Aggregation",
- "Sequence assembly visualisation",
- "Read mapping",
- "Sequence contamination filtering"
+ "Scatter plot plotting",
+ "Box-Whisker plot plotting"
],
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@@ -132866,7 +116763,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -132889,7 +116785,7 @@
"Detect and remove human reads",
"Assemble retained reads and explore the results"
],
- "pageviews": 6187143,
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"How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
@@ -132934,22 +116830,22 @@
],
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+ "collapse_dataset",
+ "minimap2",
+ "bandage_image",
+ "fastp",
+ "unicycler",
"fasta_filter_by_length",
- "samtools_view",
- "seqtk_sample",
- "bowtie2",
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+ "samtools_stats",
"nanoplot",
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- "bandage_info",
- "unicycler",
- "fastp",
- "samtools_stats",
- "bandage_image",
"__ZIP_COLLECTION__",
- "collapse_dataset"
+ "bowtie2",
+ "seqtk_sample"
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"url": "https://usegalaxy.no/",
@@ -133021,6 +116912,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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},
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{
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"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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{
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"state": "local"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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"2.5.0+galaxy0",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -134967,6 +118783,10 @@
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{
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@@ -134991,8 +118811,8 @@
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- "1.9"
+ "1.9",
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]
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{
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@@ -135128,6 +118939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -135182,10 +118997,6 @@
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{
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@@ -135283,6 +119089,10 @@
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{
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{
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"state": "inexact",
@@ -135457,6 +119241,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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@@ -135510,10 +119298,6 @@
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{
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@@ -135562,11 +119346,6 @@
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{
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"state": "exact",
@@ -135612,6 +119391,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -135668,10 +119451,6 @@
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{
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@@ -135721,14 +119500,6 @@
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- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -135797,7 +119568,7 @@
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"visit_duration": 368,
- "visitors": 2247111,
+ "visitors": 2257953,
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{
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@@ -135883,7 +119654,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Samtools fastx\"];\n 7 -->|outputsam| 10;\n 11[\"Samtools fastx\"];\n 9 -->|outputsam| 11;\n 12[\"Collapse Collection\"];\n 10 -->|nonspecific| 12;\n 13[\"Zip Collection\"];\n 11 -->|forward| 13;\n 11 -->|reverse| 13;\n 14[\"Collapse Collection\"];\n 11 -->|forward| 14;\n 15[\"Collapse Collection\"];\n 11 -->|reverse| 15;\n 16[\"seqtk_sample\"];\n 14 -->|output| 16;\n 17[\"seqtk_sample\"];\n 15 -->|output| 17;\n 18[\"Create assemblies with Unicycler\"];\n 12 -->|output| 18;\n 16 -->|default| 18;\n 17 -->|default| 18;\n 19[\"Bandage Info\"];\n 18 -->|assembly_graph| 19;\n 2[\"fastp: Trimmed Illumina Reads\"];\n 0 -->|output| 2;\n 20[\"Filter sequences by length\"];\n 18 -->|assembly| 20;\n 21[\"Bandage Image\"];\n 18 -->|assembly_graph| 21;\n 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 4[\"Map with minimap2\"];\n 1 -->|output| 4;\n 5[\"MultiQC\"];\n 2 -->|report_json| 5;\n 6[\"Bowtie2\"];\n 2 -->|output_paired_coll| 6;\n 7[\"Samtools view\"];\n 4 -->|alignment_output| 7;\n 8[\"Samtools stats\"];\n 4 -->|alignment_output| 8;\n 9[\"Samtools view\"];\n 6 -->|output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "assembly_with_preprocessing",
"outputs": [
{
@@ -136809,7 +120580,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Samtools stats\"];\n 6 -->|alignment_output| 10;\n 11[\"Samtools view\"];\n 8 -->|output| 11;\n 12[\"Samtools fastx\"];\n 9 -->|outputsam| 12;\n 13[\"Samtools fastx\"];\n 11 -->|outputsam| 13;\n 14[\"Collapse Collection\"];\n 12 -->|nonspecific| 14;\n 15[\"Zip Collection\"];\n 13 -->|forward| 15;\n 13 -->|reverse| 15;\n 16[\"Collapse Collection\"];\n 13 -->|forward| 16;\n 17[\"Collapse Collection\"];\n 13 -->|reverse| 17;\n 18[\"seqtk_sample\"];\n 16 -->|output| 18;\n 19[\"seqtk_sample\"];\n 17 -->|output| 19;\n 2[\"Illumina data\"];\n 0 -->|output| 2;\n 20[\"Create assemblies with Unicycler\"];\n 14 -->|output| 20;\n 18 -->|default| 20;\n 19 -->|default| 20;\n 21[\"Bandage Info\"];\n 20 -->|assembly_graph| 21;\n 22[\"Bandage Image\"];\n 20 -->|assembly_graph| 22;\n 23[\"Filter sequences by length\"];\n 20 -->|assembly| 23;\n 3[\"ONT data\"];\n 1 -->|output| 3;\n 4[\"fastp: Trimmed Illumina Reads\"];\n 2 -->|list_paired| 4;\n 5[\"NanoPlot\"];\n 3 -->|output_collection| 5;\n 6[\"Map with minimap2\"];\n 3 -->|output_collection| 6;\n 7[\"MultiQC\"];\n 4 -->|report_json| 7;\n 8[\"Bowtie2\"];\n 4 -->|output_paired_coll| 8;\n 9[\"Samtools view\"];\n 6 -->|alignment_output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "assembly_with_preprocessing_and_sra_download",
"outputs": [
{
@@ -137847,93 +121618,7 @@
},
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@@ -137954,16 +121639,15 @@
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"Data handling",
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],
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@@ -137999,7 +121683,7 @@
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],
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@@ -138023,24 +121707,19 @@
],
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"tp_replace_in_line",
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@@ -138112,6 +121791,10 @@
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},
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"url": "https://usegalaxy.no/",
@@ -138266,6 +121940,10 @@
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -139165,6 +122812,10 @@
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@@ -139320,6 +122962,10 @@
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{
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@@ -139353,8 +122999,8 @@
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"0.39+galaxy0",
+ "0.38.1",
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]
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@@ -139378,10 +123024,6 @@
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{
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@@ -139429,31 +123071,26 @@
"0.38.1",
"0.36.4",
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+ "0.36.0",
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+ "0.32.2"
]
},
{
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"state": "inexact",
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"0.39+galaxy0",
+ "0.38.1",
"0.36.4",
"0.39+galaxy2",
"0.36.5",
"0.32.3",
+ "0.36.0",
"0.32.1",
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+ "0.32.2"
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@@ -139506,6 +123143,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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{
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{
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@@ -139603,8 +123240,8 @@
"server": "https://usegalaxy.be/",
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"versions": [
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"0.36.6",
+ "0.38.0",
"0.39+galaxy2",
"0.36.5",
"0.32.3"
@@ -139620,11 +123257,6 @@
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{
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@@ -139689,7 +123321,7 @@
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"video_view": 0,
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- "visitors": 3554,
+ "visitors": 3559,
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@@ -139759,7 +123391,7 @@
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+ "modified": "2024-12-13 13:26:18 +0000",
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"outputs": [
{
@@ -140607,15 +124239,15 @@
],
"dir": "topics/variant-analysis/tutorials/sars-cov-2",
"edam_operation": [
- "Data handling",
+ "Validation",
"Sequencing quality control",
"Formatting",
- "Sequence alignment",
- "Validation",
+ "Data handling",
"SNP detection",
- "Read mapping",
- "Generation",
"Sequence contamination filtering",
+ "Generation",
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+ "Sequence alignment",
"Genome indexing"
],
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@@ -140631,7 +124263,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -140653,7 +124284,7 @@
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"Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
],
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+ "pageviews": 19161,
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"questions": [
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@@ -140676,20 +124307,20 @@
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- "Grep1",
- "snpeff_sars_cov_2",
- "tp_cut_tool",
- "lofreq_viterbi",
+ "Filter1",
+ "fastp",
"lofreq_indelqual",
+ "lofreq_viterbi",
"lofreq_call",
+ "bwa_mem",
"multiqc",
- "Filter1",
- "snpSift_extractFields",
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+ "picard_MarkDuplicates",
+ "tp_cut_tool",
+ "snpeff_sars_cov_2",
"fasterq_dump",
- "fastp",
"samtools_stats",
- "bwa_mem"
+ "snpSift_extractFields"
],
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@@ -140723,11 +124354,6 @@
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{
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"url": "https://usegalaxy.no/",
@@ -140762,6 +124388,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -140817,10 +124447,6 @@
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -140867,11 +124493,6 @@
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},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
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"url": "https://usegalaxy.no/",
@@ -140916,6 +124537,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
+ },
{
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@@ -141058,6 +124675,10 @@
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},
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{
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{
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@@ -141355,6 +124963,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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{
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@@ -141676,6 +125274,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -141736,10 +125338,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -141788,11 +125386,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -141838,6 +125431,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -141895,10 +125492,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -141947,11 +125540,6 @@
"state": "exact",
"version": "0.20.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142000,6 +125588,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142055,10 +125647,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -142107,11 +125695,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142157,6 +125740,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142209,10 +125796,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -142261,11 +125844,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142311,6 +125889,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142363,10 +125945,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -142411,11 +125989,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142461,6 +126034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142486,9 +126063,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -142525,10 +126102,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -142578,11 +126151,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142628,6 +126196,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142681,10 +126253,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -142729,11 +126297,6 @@
"state": "exact",
"version": "4.5covid19"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.5covid19"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142779,6 +126342,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142833,10 +126400,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -142881,11 +126444,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -142931,6 +126489,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -142986,10 +126548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -143036,28 +126594,6 @@
"state": "exact",
"version": "2.10.7+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.1+galaxy0",
- "2.10.4",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.8+galaxy0",
- "3.0.5+galaxy0",
- "2.10.7+galaxy2",
- "3.0.3+galaxy0",
- "2.11.0+galaxy1",
- "3.1.1+galaxy1",
- "3.0.8+galaxy0",
- "3.1.0+galaxy1",
- "3.0.10+galaxy0",
- "3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -143076,24 +126612,24 @@
"versions": [
"2.10.9+galaxy0",
"3.1.1+galaxy0",
+ "2.11.0+galaxy0",
"2.10.4",
"2.10.4+galaxy1",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.4+galaxy2",
"2.10.8+galaxy0",
- "2.10.7+galaxy0",
+ "2.10.4+galaxy2",
"3.0.5+galaxy0",
+ "2.10.7+galaxy0",
"3.0.3+galaxy0",
+ "3.0.5+galaxy3",
+ "3.0.8+galaxy1",
"2.11.0+galaxy1",
"3.1.1+galaxy1",
"3.0.8+galaxy0",
"3.1.0+galaxy1",
- "3.0.10+galaxy0",
"3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0",
- "3.0.5+galaxy1"
+ "3.0.10+galaxy0",
+ "3.0.5+galaxy1",
+ "3.0.0+galaxy0"
]
},
{
@@ -143126,6 +126662,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -143181,10 +126721,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -143220,10 +126756,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.10.4",
- "2.10.4+galaxy1",
"2.10.7+galaxy1",
- "2.11.0+galaxy0"
+ "2.11.0+galaxy0",
+ "2.10.4",
+ "2.10.4+galaxy1"
]
},
{
@@ -143236,11 +126772,6 @@
"state": "exact",
"version": "3.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -143312,7 +126843,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 175,
- "visitors": 12594,
+ "visitors": 12606,
"workflows": [
{
"creators": [],
@@ -143443,7 +126974,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Faster Download and Extract Reads in FASTQ\"];\n 1 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|list_paired| 3;\n 4[\"Map with BWA-MEM\"];\n 3 -->|output_paired_coll| 4;\n 0 -->|output| 4;\n 5[\"MarkDuplicates\"];\n 4 -->|bam_output| 5;\n 6[\"Realign reads\"];\n 5 -->|outFile| 6;\n 0 -->|output| 6;\n 7[\"Samtools stats\"];\n 5 -->|outFile| 7;\n 8[\"Insert indel qualities\"];\n 6 -->|realigned| 8;\n 0 -->|output| 8;\n 2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n 8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n 9[\"Call variants\"];\n 8 -->|output| 9;\n 0 -->|output| 9;\n 10[\"SnpEff eff:\"];\n 9 -->|variants| 10;\n 11[\"SnpSift Extract Fields\"];\n 10 -->|snpeff_output| 11;\n 06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n 11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n 12[\"MultiQC\"];\n 3 -->|report_json| 12;\n 7 -->|output| 12;\n 5 -->|metrics_file| 12;\n 10 -->|csvFile| 12;\n 758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n 12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Simple COVID-19 - PE Variation",
"outputs": [
{
@@ -144202,8 +127733,8 @@
"edam_operation": [
"Methylation analysis",
"Variant classification",
- "Tree-based sequence alignment",
- "Variant calling"
+ "Variant calling",
+ "Tree-based sequence alignment"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -144238,7 +127769,7 @@
"Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
"Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
],
- "pageviews": 12244,
+ "pageviews": 12257,
"pub_date": "2021-06-30",
"questions": [
"How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -144301,12 +127832,12 @@
],
"short_id": "T00316",
"short_tools": [
+ "Filter1",
"datamash_ops",
- "pangolin",
"nextclade",
"fasta_regex_finder",
- "Filter1",
- "upload1"
+ "upload1",
+ "pangolin"
],
"slides": false,
"slides_recordings": false,
@@ -144354,6 +127885,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -144409,10 +127944,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -144459,11 +127990,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -144508,6 +128034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -144560,10 +128090,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -144604,10 +128130,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -144650,6 +128172,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -144710,10 +128236,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -144761,11 +128283,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -144816,6 +128333,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -144869,10 +128390,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -144916,11 +128433,6 @@
"state": "exact",
"version": "2.7.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -144965,6 +128477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -144997,11 +128513,11 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
"3.0.3+galaxy0",
+ "4.1.1+galaxy0",
"4.0.5+galaxy0",
- "4.1.1+galaxy0"
+ "3.1.16+galaxy0",
+ "4.1.2+galaxy0"
]
},
{
@@ -145024,10 +128540,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -145077,11 +128589,6 @@
"state": "exact",
"version": "4.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -145126,6 +128633,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -145178,10 +128689,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -145224,10 +128731,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -145271,6 +128774,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -145323,10 +128830,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -145367,10 +128870,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -145427,8 +128926,8 @@
"video": true,
"video_versions": 3,
"video_view": 0,
- "visit_duration": 208,
- "visitors": 6643
+ "visit_duration": 209,
+ "visitors": 6653
},
{
"admin_install": {
@@ -145489,19 +128988,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: ddf54b12c295\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqtofasta\n owner: devteam\n revisions: 297962e79f39\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jq\n owner: iuc\n revisions: 5ff75eb1a893\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n owner: iuc\n revisions: 2a3a00c1fa0a\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n owner: iuc\n revisions: 69ebb7f46e45\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n owner: iuc\n revisions: 83c7d564b128\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
- "contributions": {
- "authorship": [
- "jontrow",
- "RareSeas"
- ],
- "reviewing": [
- "shiltemann",
- "mtekman",
- "hexylena",
- "bgruening",
- "natefoo"
- ]
- },
"contributors": [
{
"github": false,
@@ -145517,125 +129003,6 @@
"name": "Adelaide Rhodes",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/RareSeas/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/RareSeas.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "nate@bx.psu.edu",
- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
}
],
"dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
@@ -145673,7 +129040,7 @@
"Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
"Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
],
- "pageviews": 5424193,
+ "pageviews": 5447169,
"pub_date": "2021-05-31",
"questions": [
"How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
@@ -145705,13 +129072,13 @@
],
"short_id": "T00155",
"short_tools": [
- "snpeff_sars_cov_2",
- "tp_cat",
- "fastq_dump",
- "fasterq_dump",
+ "jq",
"query_tabular",
"fastq_to_fasta_python",
- "jq"
+ "tp_cat",
+ "fasterq_dump",
+ "snpeff_sars_cov_2",
+ "fastq_dump"
],
"slides": true,
"slides_recordings": [
@@ -145787,6 +129154,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -145842,10 +129213,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -145892,11 +129259,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -145941,6 +129303,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -145995,10 +129361,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -146045,11 +129407,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -146095,6 +129452,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146148,10 +129509,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -146195,10 +129552,6 @@
"state": "exact",
"version": "1.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -146244,6 +129597,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146296,10 +129653,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -146343,11 +129696,6 @@
"state": "exact",
"version": "1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -146393,6 +129741,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146451,10 +129803,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -146501,18 +129849,6 @@
"state": "exact",
"version": "3.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.1",
- "3.3.0",
- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -146558,6 +129894,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146611,10 +129951,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -146659,11 +129995,6 @@
"state": "exact",
"version": "4.5covid19"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.5covid19"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -146709,6 +130040,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146764,10 +130099,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -146809,16 +130140,16 @@
"state": "inexact",
"versions": [
"2.10.9+galaxy0",
+ "2.10.7+galaxy1",
"2.10.4",
"2.10.4+galaxy1",
- "2.10.7+galaxy1",
- "3.0.5+galaxy3",
- "2.10.4+galaxy2",
"2.10.8+galaxy0",
- "2.10.7+galaxy0",
+ "2.10.4+galaxy2",
"3.0.5+galaxy0",
"2.10.7+galaxy2",
- "3.0.3+galaxy0"
+ "2.10.7+galaxy0",
+ "3.0.3+galaxy0",
+ "3.0.5+galaxy3"
]
},
{
@@ -146826,11 +130157,6 @@
"state": "exact",
"version": "2.11.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.11.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -146878,6 +130204,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -146936,10 +130266,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -146983,16 +130309,16 @@
"2.9.1.3",
"2.10.9+galaxy0",
"2.10.4",
- "2.10.7+galaxy1",
"2.8.0",
"2.10.4+galaxy1",
- "3.0.3+galaxy0",
- "2.10.8+galaxy0",
- "3.0.5+galaxy3",
- "1.2.5",
+ "2.10.7+galaxy1",
+ "2.10.7+galaxy2",
"2.10.7+galaxy0",
+ "1.2.5",
+ "2.10.8+galaxy0",
"3.0.5+galaxy0",
- "2.10.7+galaxy2"
+ "3.0.5+galaxy3",
+ "3.0.3+galaxy0"
]
},
{
@@ -147000,22 +130326,17 @@
"state": "inexact",
"versions": [
"3.1.1+galaxy0",
- "3.0.3+galaxy0",
- "3.0.5+galaxy3",
"3.0.5+galaxy0",
- "3.0.10+galaxy0",
- "3.0.8+galaxy0",
- "3.1.0+galaxy0",
- "3.1.0+galaxy1",
+ "3.0.5+galaxy3",
+ "3.0.3+galaxy0",
"3.0.8+galaxy1",
- "3.1.1+galaxy1"
+ "3.1.1+galaxy1",
+ "3.1.0+galaxy1",
+ "3.1.0+galaxy0",
+ "3.0.8+galaxy0",
+ "3.0.10+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.11.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -147075,8 +130396,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 260,
- "visitors": 2019505
+ "visit_duration": 259,
+ "visitors": 2029550
},
{
"admin_install": {
@@ -147332,19 +130653,18 @@
],
"dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
"edam_operation": [
+ "Sequence alignment",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
"Sequence composition calculation",
- "Read mapping",
"Generation",
+ "Read mapping",
"Genome visualisation",
"Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -147378,7 +130698,7 @@
"Critique large data sets and use bioinformatics to assess genetics data",
"Tap into the interdisciplinary nature of science"
],
- "pageviews": 1042,
+ "pageviews": 1050,
"pub_date": "2023-07-10",
"questions": [
"How do I check my data quality?",
@@ -147387,8 +130707,8 @@
],
"short_id": "T00356",
"short_tools": [
- "jbrowse",
"fastqc",
+ "jbrowse",
"bwa_mem"
],
"slides": false,
@@ -147400,11 +130720,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -147476,6 +130791,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -147531,10 +130850,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -147581,11 +130896,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -147630,6 +130940,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -147689,10 +131003,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -147740,11 +131050,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -147791,6 +131096,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -147848,10 +131157,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -147877,8 +131182,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -147902,12 +131207,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -147917,9 +131222,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -147930,11 +131235,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -147980,6 +131280,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -148040,10 +131344,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -148092,11 +131392,6 @@
"state": "exact",
"version": "1.16.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -148153,8 +131448,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 255,
- "visitors": 808,
+ "visit_duration": 256,
+ "visitors": 815,
"zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
},
{
@@ -148357,15 +131652,15 @@
"layout": "tutorial_hands_on",
"level": "Introductory",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Familiarize yourself with data manipulation tools in Galaxy",
"Perform basic text manipulation tasks in Galaxy",
"Become comfortable converting text-based files in a variety of ways.",
"Reason about the expected outcome of tools"
],
- "pageviews": 0,
- "pub_date": "2024-12-09",
+ "pageviews": 1,
+ "pub_date": "2024-12-13",
"questions": [
"How can I do basic data manipulation in Galaxy?",
"Which tools are available to convert, reformat, filter, sort etc my text-based data?"
@@ -148373,24 +131668,24 @@
"short_id": "T00077",
"short_tools": [
"",
- "datamash_ops",
- "tp_cat",
- "Add_a_column1",
+ "cat1",
"tp_sort_header_tool",
- "tp_sorted_uniq",
- "upload1",
- "Grouping1",
- "Remove beginning1",
"Filter1",
- "join1",
"Cut1",
- "tp_split_on_column",
- "cat1",
"Show beginning1",
- "regexColumn1",
+ "Add_a_column1",
+ "tp_cat",
"Count1",
+ "tp_split_on_column",
+ "regexColumn1",
+ "tp_sorted_uniq",
"tabular_to_csv",
- "wc_gnu"
+ "Remove beginning1",
+ "datamash_ops",
+ "wc_gnu",
+ "Grouping1",
+ "join1",
+ "upload1"
],
"slides": false,
"slides_recordings": false,
@@ -148421,6 +131716,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -148476,10 +131775,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -148526,11 +131821,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -148575,6 +131865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -148627,10 +131921,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -148671,10 +131961,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -148717,6 +132003,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -148769,10 +132059,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -148813,10 +132099,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -148859,6 +132141,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -148911,10 +132197,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -148955,10 +132237,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149001,6 +132279,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149053,10 +132335,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149097,10 +132375,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149143,6 +132417,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149195,10 +132473,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149239,10 +132513,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149285,6 +132555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149337,10 +132611,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149381,10 +132651,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149427,6 +132693,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149479,10 +132749,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149523,10 +132789,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149569,6 +132831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149621,10 +132887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149665,10 +132927,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149711,6 +132969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -149763,10 +133025,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -149807,10 +133065,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -149853,6 +133107,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -149908,10 +133166,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -149954,11 +133208,6 @@
"state": "exact",
"version": "0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150006,6 +133255,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150060,10 +133313,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150112,11 +133361,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150162,6 +133406,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150216,10 +133464,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150266,11 +133510,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150316,6 +133555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150370,10 +133613,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150420,11 +133659,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150470,6 +133704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150527,10 +133765,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150566,9 +133800,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -150576,8 +133810,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -150586,11 +133820,6 @@
"state": "exact",
"version": "1.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150636,6 +133865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150692,10 +133925,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150744,11 +133973,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -150796,6 +134020,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -150853,10 +134081,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -150903,11 +134127,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -150953,6 +134172,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -151012,10 +134235,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -151070,11 +134289,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -151120,6 +134334,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -151172,10 +134390,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -151216,10 +134430,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -151262,6 +134472,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -151314,10 +134528,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -151358,10 +134568,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -154004,7 +137138,7 @@
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"video_view": 0,
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- "visitors": 0,
+ "visitors": 1,
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@@ -154099,7 +137233,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
"outputs": [],
"parent_id": "data-science/data-manipulation-olympics",
@@ -154313,7 +137447,6 @@
"Galaxy@AuBi",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -154348,7 +137481,7 @@
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],
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+ "pageviews": 1651327,
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"questions": [
"How to employ bioinformatics resources to investigate a specific protein family (opsins)?",
@@ -154380,11 +137513,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -154451,6 +137579,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -154506,10 +137638,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -154556,11 +137684,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -154605,6 +137728,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -154639,8 +137766,8 @@
"state": "inexact",
"versions": [
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- "2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.14.1+galaxy2"
]
},
{
@@ -154663,10 +137790,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -154709,8 +137832,8 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.14.1+galaxy2",
"0.3.3",
+ "2.14.1+galaxy2",
"0.0.11",
"0.1.07",
"0.3.0"
@@ -154726,11 +137849,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -154786,7 +137904,7 @@
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"video_view": 0,
"visit_duration": 358,
- "visitors": 674473,
+ "visitors": 683998,
"zenodo_link": "https://zenodo.org/record/8304465"
},
{
@@ -154948,7 +138066,7 @@
"objectives": [
"Have a basic understanding of history of biology from Darwin to today."
],
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+ "pageviews": 1300997,
"priority": 1,
"pub_date": "2024-01-09",
"questions": [
@@ -155024,7 +138142,7 @@
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"video_view": 0,
"visit_duration": 156,
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+ "visitors": 528806
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{
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@@ -155319,7 +138437,7 @@
"Use the output of one command as the command-line argument(s) to another command.",
"Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well."
],
- "pageviews": 897,
+ "pageviews": 901,
"pub_date": "2021-09-30",
"questions": [
"How can I combine existing commands to do new things?",
@@ -155404,8 +138522,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 127,
- "visitors": 722,
+ "visit_duration": 128,
+ "visitors": 726,
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},
{
@@ -155417,20 +138535,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json",
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@@ -155485,110 +138589,6 @@
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
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],
"dir": "topics/data-science/tutorials/sql-r",
@@ -155630,7 +138630,7 @@
"Trace the execution of a program that contains an SQL query.",
"Explain why most database applications are written in a general-purpose language rather than in SQL."
],
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+ "pageviews": 716,
"pub_date": "2021-10-11",
"questions": [
"How can I access databases from programs written in R?"
@@ -155721,8 +138721,8 @@
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+ "visit_duration": 33,
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{
@@ -155737,21 +138737,6 @@
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@@ -155806,136 +138791,6 @@
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- "lon": 3.08
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}
],
"dir": "topics/data-science/tutorials/sql-advanced",
@@ -156024,7 +138879,7 @@
"Trace the execution of a program that contains an SQL query.",
"Explain why most database applications are written in a general-purpose language rather than in SQL."
],
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+ "pageviews": 1724,
"pub_date": "2021-10-11",
"questions": [
"How can I calculate sums, averages, and other summary values?",
@@ -156121,7 +138976,7 @@
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{
@@ -156137,21 +138992,6 @@
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@@ -156220,136 +139060,6 @@
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- "matrix": "abretaud:matrix.org",
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@@ -172731,32 +152331,6 @@
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@@ -172912,246 +152486,6 @@
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@@ -173194,7 +152528,7 @@
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@@ -173506,7 +152670,7 @@
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@@ -173602,186 +152750,6 @@
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],
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"twitter": "jmchilton",
"url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
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"Learn to write API tests",
"Learn to write unit tests"
],
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+ "pageviews": 637,
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 165,
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+ "visit_duration": 170,
+ "visitors": 211
},
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},
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"api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json",
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{
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"twitter": "bebatut",
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- "twitter": "natefoo",
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- "fediverse": "https://mastodon.world/@martenson",
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- "joined": "2017-09",
- "location": {
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- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
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"edam_operation": [],
"edam_topic": [],
"exact_supported_servers": [
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -177039,7 +154456,7 @@
"Partition occurrence data",
"Model a theoretical ecological niche and predict species distribution in a future climate scenario by using SDM"
],
- "pageviews": 4282,
+ "pageviews": 4294,
"pub_date": "2019-07-04",
"questions": [
"How to build & evaluate a niche model, visualize and project it?"
@@ -177047,12 +154464,12 @@
"requirements": null,
"short_id": "T00135",
"short_tools": [
- "tp_find_and_replace",
- "spocc_occ",
- "tp_cut_tool",
"Filter1",
+ "interactive_tool_wallace",
"tabular_to_csv",
- "interactive_tool_wallace"
+ "tp_find_and_replace",
+ "spocc_occ",
+ "tp_cut_tool"
],
"slides": false,
"slides_recordings": false,
@@ -177063,11 +154480,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
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- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": []
@@ -177094,6 +154506,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -177149,10 +154565,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -177199,11 +154611,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -177248,6 +154655,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -177300,10 +154711,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -177344,10 +154751,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -177390,6 +154793,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -177442,10 +154849,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -177486,10 +154889,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -177532,6 +154931,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -177584,10 +154987,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -177628,10 +155027,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -177674,6 +155069,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -177728,10 +155127,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -177779,11 +155174,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -177829,6 +155219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -177853,8 +155247,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.1.4",
- "1.1.3"
+ "1.1.3",
+ "1.1.4"
]
},
{
@@ -177865,8 +155259,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.1.4",
- "1.1.3"
+ "1.1.3",
+ "1.1.4"
]
},
{
@@ -177889,10 +155283,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -177933,8 +155323,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.1.4",
"1.1.3",
+ "1.1.4",
"1.1.0"
]
},
@@ -177943,18 +155333,13 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
- "1.1.1"
+ "1.1.1",
+ "1.1.0"
]
},
{
@@ -177966,8 +155351,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.1.4",
"1.1.3",
+ "1.1.4",
"9.3+galaxy1",
"1.1.1",
"9.3+galaxy0"
@@ -178003,6 +155388,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -178055,10 +155444,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -178102,11 +155487,6 @@
"state": "exact",
"version": "0.9.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.9.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -178166,7 +155546,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 68,
- "visitors": 2731,
+ "visitors": 2742,
"workflows": [
{
"creators": [],
@@ -178211,7 +155591,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"Get species occurrences data\"];\n 1[\"Wallace\"];\n 2[\"Cut\"];\n 0 -->|output| 2;\n 3[\"Filter\"];\n 2 -->|output| 3;\n 4[\"Convert tabular to CSV\"];\n 3 -->|out_file1| 4;\n 5[\"Replace\"];\n 4 -->|csv| 5;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Species Distribution Modeling With Wallace From GBIF - Training Material",
"outputs": [
{
@@ -178357,21 +155737,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: 74a8bef53a00\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n owner: devteam\n revisions: 64f11cf59c6e\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_wrappers\n owner: devteam\n revisions: b4427dbb6ced\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: ff9530579d1f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: 1c2db0054039\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n owner: iuc\n revisions: 45db1ba16163\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n owner: iuc\n revisions: eded025438db\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_refmap\n owner: iuc\n revisions: d7a482f44e08\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_replace\n owner: kellrott\n revisions: 9a77d5fca67c\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json",
- "contributions": {
- "authorship": [
- "yvanlebras"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "nsoranzo",
- "yvanlebras",
- "bebatut",
- "bgruening",
- "willdurand",
- "njall"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -178391,188 +155756,18 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
"twitter": "Yvan2935",
"url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
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- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
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- "pndb",
- "gallantries",
- "fairease",
- "fnso2019",
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "email": "yvan.le-bras@mnhn.fr",
- "id": "yvanlebras",
- "joined": "2017-09",
- "matrix": "yvanlebras:matrix.org",
- "name": "Yvan Le Bras",
- "orcid": "0000-0002-8504-068X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
- "twitter": "Yvan2935",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "id": "willdurand",
- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/ecology/tutorials/ref-based-rad-seq",
"edam_operation": [
- "Data handling",
+ "Validation",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
- "Validation",
"Sequence composition calculation",
- "Read mapping",
+ "Data handling",
"Generation",
+ "Read mapping",
+ "Sequence alignment",
"Genome indexing"
],
"edam_topic": [],
@@ -178595,7 +155790,7 @@
"SNP calling from RAD sequencing data",
"Calculate population genomics statistics from RAD sequencing data"
],
- "pageviews": 3933,
+ "pageviews": 3950,
"pub_date": "2017-02-14",
"questions": [
"How to analyze RAD sequencing data using a reference genome for a population genomics study?"
@@ -178607,24 +155802,24 @@
],
"short_id": "T00133",
"short_tools": [
- "Grep1",
- "regex_replace",
- "addValue",
- "Convert characters1",
- "fastqc",
- "bwa_wrapper",
- "stacks_refmap",
- "bwa",
- "tp_replace_in_line",
- "Filter1",
- "multiqc",
- "tp_sort_header_tool",
"stacks_procrad",
- "Count1",
"cat1",
+ "tp_sort_header_tool",
+ "Filter1",
"Cut1",
+ "bwa",
+ "Convert characters1",
+ "tp_replace_in_line",
+ "fastqc",
+ "Count1",
+ "multiqc",
+ "Grep1",
+ "bwa_wrapper",
"stacks_populations",
- "Summary_Statistics1"
+ "regex_replace",
+ "Summary_Statistics1",
+ "addValue",
+ "stacks_refmap"
],
"slides": false,
"slides_recordings": false,
@@ -178655,6 +155850,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -178710,10 +155909,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -178760,11 +155955,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -178809,6 +155999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -178861,10 +156055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -178905,10 +156095,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -178951,6 +156137,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179003,10 +156193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179047,10 +156233,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179093,6 +156275,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179145,10 +156331,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179189,10 +156371,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179235,6 +156413,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179287,10 +156469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179331,10 +156509,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179377,6 +156551,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179429,10 +156607,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179473,10 +156647,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179519,6 +156689,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179571,10 +156745,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179615,10 +156785,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179661,6 +156827,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179713,10 +156883,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179757,10 +156923,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179803,6 +156965,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -179855,10 +157021,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -179899,10 +157061,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -179945,6 +157103,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -180003,10 +157165,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -180056,15 +157214,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.2",
- "9.3+galaxy1",
- "9.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -180110,6 +157259,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -180164,10 +157317,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -180214,11 +157363,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -180264,6 +157408,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -180321,10 +157469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -180372,11 +157516,6 @@
"state": "exact",
"version": "0.7.17.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -180425,6 +157564,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -180477,10 +157620,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -180521,10 +157660,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -180567,6 +157702,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -180592,8 +157731,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -180632,10 +157771,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -180686,9 +157821,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -180699,17 +157834,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "0.73+galaxy0",
- "0.72",
- "0.74+galaxy0",
- "0.74+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -180759,186 +157883,176 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
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- {
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
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- {
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- "state": "exact",
- "version": "1.6"
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- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
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- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1"
- ]
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
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- {
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- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
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- ]
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- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
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- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
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- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1"
- ]
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "1.9",
- "1.8+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.6"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.6"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy1",
- "1.24.1+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
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- "1.7",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
- ]
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- {
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- "state": "exact",
- "version": "1.6"
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- {
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- "state": "exact",
- "version": "1.6"
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- {
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- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "1.6"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1",
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1"
+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "1.9",
+ "1.8+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "1.6"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.6"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1",
+ "1.9",
+ "1.8+galaxy0",
+ "1.8+galaxy2",
+ "1.8+galaxy1",
+ "1.7.1"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.6"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.6"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.6"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -180993,10 +158107,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -181042,13 +158152,6 @@
"state": "exact",
"version": "1.46.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.46.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -181100,6 +158203,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -181152,10 +158259,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -181199,11 +158302,6 @@
"state": "exact",
"version": "1.46.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.46.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -181248,6 +158346,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -181300,10 +158402,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -181347,11 +158445,6 @@
"state": "exact",
"version": "1.46.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.46.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -181396,6 +158489,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -181448,10 +158545,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -181495,11 +158588,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -181571,8 +158659,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 103,
- "visitors": 2385,
+ "visit_duration": 102,
+ "visitors": 2399,
"workflows": [
{
"creators": [],
@@ -181729,7 +158817,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"FastQC\"];\n 5 -->|demultiplexed| 10;\n 11[\"Map with BWA\"];\n 5 -->|demultiplexed| 11;\n 3 -->|output| 11;\n 12[\"Select\"];\n 6 -->|output_log| 12;\n 13[\"Select\"];\n 6 -->|output_log| 13;\n 14[\"Replace Text\"];\n 7 -->|outfile| 14;\n 15[\"Replace Text\"];\n 8 -->|out_file1| 15;\n 16[\"Replace Text\"];\n 9 -->|out_file1| 16;\n 17[\"MultiQC\"];\n 10 -->|text_file| 17;\n 18[\"Replace Text\"];\n 12 -->|out_file1| 18;\n 19[\"Replace Text\"];\n 13 -->|out_file1| 19;\n 2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 20[\"Add column\"];\n 14 -->|outfile| 20;\n 21[\"Concatenate datasets\"];\n 19 -->|outfile| 21;\n 15 -->|outfile| 21;\n 16 -->|outfile| 21;\n 18 -->|outfile| 21;\n 22[\"Cut\"];\n 20 -->|out_file1| 22;\n 23[\"Convert\"];\n 21 -->|out_file1| 23;\n 24[\"Regex Replace\"];\n 22 -->|out_file1| 24;\n 25[\"Stacks: reference map\"];\n 11 -->|bam_output| 25;\n 24 -->|outfile| 25;\n 26[\"Stacks: populations\"];\n 25 -->|all_output| 26;\n 24 -->|outfile| 26;\n 27[\"Summary Statistics\"];\n 26 -->|out_fstats| 27;\n 28[\"Sort\"];\n 26 -->|out_fstats| 28;\n 29[\"Count\"];\n 26 -->|out_fstats| 29;\n 3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 30[\"Filter\"];\n 26 -->|out_fstats| 30;\n 4[\"Stacks: process radtags\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n 5[\"Stacks: process radtags\"];\n 1 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Stacks: process radtags\"];\n 1 -->|output| 6;\n 0 -->|output| 6;\n 7[\"Replace Text\"];\n 2 -->|output| 7;\n 8[\"Select\"];\n 4 -->|output_log| 8;\n 9[\"Select\"];\n 5 -->|output_log| 9;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
"outputs": [],
"parent_id": "ecology/ref-based-rad-seq",
@@ -181925,7 +159013,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Stacks: process radtags\"];\n 2 -->|output| 4;\n 3 -->|output| 4;\n 5[\"Stacks: process radtags\"];\n 2 -->|output| 5;\n 3 -->|output| 5;\n 6[\"Stacks: process radtags\"];\n 2 -->|output| 6;\n 3 -->|output| 6;\n 7[\"Map with BWA for Illumina\"];\n 0 -->|output| 7;\n 4 -->|demultiplexed| 7;\n 8[\"Stacks: reference map\"];\n 7 -->|output| 8;\n 1 -->|output| 8;\n 9[\"Stacks: populations\"];\n 8 -->|all_output| 9;\n 1 -->|output| 9;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Ref Based Rad Seq",
"outputs": [],
"parent_id": "ecology/ref-based-rad-seq",
@@ -182317,7 +159405,6 @@
"id": "ecology/PAMPA-toolsuite-tutorial",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"js_requirements": {
@@ -182365,21 +159452,21 @@
],
"short_id": "T00125",
"short_tools": [
- "tp_easyjoin_tool",
- "regexColumn1",
- "tp_cut_tool",
- "tp_cat",
+ "tp_sort_header_tool",
"Filter1",
"mergeCols1",
- "tp_sort_header_tool",
+ "pampa_plotglm",
"pampa_glmsp",
- "pampa_communitymetrics",
- "regex1",
+ "datamash_transpose",
+ "tp_cat",
+ "tp_easyjoin_tool",
"Count1",
- "pampa_presabs",
- "pampa_plotglm",
+ "regexColumn1",
+ "tp_cut_tool",
"pampa_glmcomm",
- "datamash_transpose"
+ "regex1",
+ "pampa_presabs",
+ "pampa_communitymetrics"
],
"slides": false,
"slides_recordings": false,
@@ -182398,11 +159485,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -182432,6 +159514,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -182487,10 +159573,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -182537,11 +159619,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -182586,6 +159663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -182638,10 +159719,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -182682,10 +159759,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -182728,6 +159801,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -182780,10 +159857,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -182824,10 +159897,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -182870,6 +159939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -182924,10 +159997,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -182974,11 +160043,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -183024,6 +160088,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183078,10 +160146,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -183129,11 +160193,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -183179,6 +160238,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183233,10 +160296,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -183283,11 +160342,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -183333,6 +160387,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183387,10 +160445,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -183437,11 +160491,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -183487,6 +160536,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183539,10 +160592,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -183586,13 +160635,6 @@
"state": "exact",
"version": "1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -183636,6 +160678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183688,10 +160734,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -183734,11 +160776,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -183785,6 +160822,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183837,10 +160878,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -183883,11 +160920,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -183934,6 +160966,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -183986,10 +161022,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -184032,11 +161064,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -184083,6 +161110,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184135,10 +161166,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -184181,11 +161208,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -184229,6 +161251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184281,10 +161307,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -184327,11 +161349,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -184378,6 +161395,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184436,10 +161457,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -184488,15 +161505,6 @@
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"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3",
- "1.0.1",
- "1.0.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -184548,6 +161556,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184606,10 +161618,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -184658,15 +161666,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3",
- "1.0.1",
- "1.0.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -184718,6 +161717,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184774,10 +161777,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -184826,11 +161825,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -184878,6 +161872,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -184937,10 +161935,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -184984,11 +161978,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -185192,7 +162181,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Column Regex Find And Replace\"];\n 0 -->|output| 3;\n 4[\"Column Regex Find And Replace\"];\n 1 -->|output| 4;\n 5[\"Concatenate datasets\"];\n 2 -->|output| 5;\n 1 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Column Regex Find And Replace\"];\n 2 -->|output| 6;\n 7[\"Merge Columns\"];\n 3 -->|out_file1| 7;\n 8[\"Merge Columns\"];\n 4 -->|out_file1| 8;\n 9[\"Count\"];\n 5 -->|out_file1| 9;\n 10[\"Filter\"];\n 5 -->|out_file1| 10;\n 11[\"Merge Columns\"];\n 6 -->|out_file1| 11;\n 12[\"Regex Find And Replace\"];\n 7 -->|out_file1| 12;\n 13[\"Regex Find And Replace\"];\n 8 -->|out_file1| 13;\n 14[\"Column Regex Find And Replace\"];\n 10 -->|out_file1| 14;\n 15[\"Regex Find And Replace\"];\n 11 -->|out_file1| 15;\n 16[\"Calculate presence absence table\"];\n 12 -->|out_file1| 16;\n 17[\"Calculate presence absence table\"];\n 13 -->|out_file1| 17;\n 18[\"Merge Columns\"];\n 14 -->|out_file1| 18;\n 19[\"Calculate presence absence table\"];\n 15 -->|out_file1| 19;\n 20[\"Regex Find And Replace\"];\n 18 -->|out_file1| 20;\n 21[\"Calculate community metrics\"];\n 20 -->|out_file1| 21;\n 22[\"Column Regex Find And Replace\"];\n 20 -->|out_file1| 22;\n 23[\"Merge Columns\"];\n 22 -->|out_file1| 23;\n 24[\"Column Regex Find And Replace\"];\n 23 -->|out_file1| 24;\n 25[\"Advanced Cut\"];\n 24 -->|out_file1| 25;\n 26[\"Sort\"];\n 25 -->|output| 26;\n 27[\"Regex Find And Replace\"];\n 26 -->|outfile| 27;\n 28[\"Compute GLM on community data\"];\n 21 -->|output_community| 28;\n 27 -->|out_file1| 28;\n 29[\"Compute GLM on population data\"];\n 16 -->|output_presabs| 29;\n 27 -->|out_file1| 29;\n 30[\"Compute GLM on population data\"];\n 17 -->|output_presabs| 30;\n 27 -->|out_file1| 30;\n 31[\"Compute GLM on population data\"];\n 19 -->|output_presabs| 31;\n 27 -->|out_file1| 31;\n 32[\"Transpose\"];\n 28 -->|output_summary| 32;\n 33[\"Create a plot from GLM data\"];\n 21 -->|output_community| 33;\n 28 -->|output_summary| 33;\n 27 -->|out_file1| 33;\n 34[\"Transpose\"];\n 29 -->|output_summary| 34;\n 35[\"Create a plot from GLM data\"];\n 16 -->|output_presabs| 35;\n 29 -->|output_summary| 35;\n 27 -->|out_file1| 35;\n 36[\"Transpose\"];\n 30 -->|output_summary| 36;\n 37[\"Create a plot from GLM data\"];\n 17 -->|output_presabs| 37;\n 30 -->|output_summary| 37;\n 27 -->|out_file1| 37;\n 38[\"Transpose\"];\n 31 -->|output_summary| 38;\n 39[\"Create a plot from GLM data\"];\n 19 -->|output_presabs| 39;\n 31 -->|output_summary| 39;\n 27 -->|out_file1| 39;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
"outputs": [],
"parent_id": "ecology/PAMPA-toolsuite-tutorial",
@@ -185568,10 +162557,10 @@
],
"dir": "topics/ecology/tutorials/Obitools-metabarcoding",
"edam_operation": [
- "Sequence analysis",
+ "Sequencing quality control",
"Sequence composition calculation",
- "Statistical calculation",
- "Sequencing quality control"
+ "Sequence analysis",
+ "Statistical calculation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -185584,8 +162573,7 @@
"hands_on": true,
"id": "ecology/Obitools-metabarcoding",
"inexact_supported_servers": [
- "UseGalaxy.cz",
- "UseGalaxy.fr"
+ "UseGalaxy.cz"
],
"js_requirements": {
"mathjax": null,
@@ -185601,7 +162589,7 @@
"Deal with paired-end data to create consensus sequences",
"Clean, filter and anlayse data to obtain strong results"
],
- "pageviews": 4643,
+ "pageviews": 4656,
"pub_date": "2022-02-28",
"questions": [
"how to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools?"
@@ -185622,23 +162610,23 @@
],
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"short_tools": [
- "obi_ngsfilter",
- "obi_tab",
- "fastqc",
- "unzip",
- "obi_grep",
- "wc_gnu",
- "obi_clean",
+ "obi_illumina_pairend",
+ "fastq_groomer",
"Filter1",
+ "Cut1",
+ "obi_clean",
"obi_stat",
+ "obi_uniq",
"obi_annotate",
+ "unzip",
+ "fastqc",
"join1",
"seq_filter_by_id",
- "Cut1",
- "obi_uniq",
- "obi_illumina_pairend",
- "fastq_groomer",
- "ncbi_blastn_wrapper"
+ "obi_ngsfilter",
+ "wc_gnu",
+ "ncbi_blastn_wrapper",
+ "obi_tab",
+ "obi_grep"
],
"slides": false,
"slides_recordings": false,
@@ -185666,11 +162654,6 @@
"name": "UseGalaxy.cz",
"url": "https://usegalaxy.cz/",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -185696,6 +162679,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -185751,10 +162738,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -185801,11 +162784,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -185850,6 +162828,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -185902,10 +162884,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -185946,10 +162924,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -185992,6 +162966,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -186044,10 +163022,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -186088,10 +163062,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -186134,6 +163104,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -186186,10 +163160,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -186230,10 +163200,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -186276,6 +163242,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -186329,10 +163299,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -186377,11 +163343,6 @@
"state": "exact",
"version": "1.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -186427,6 +163388,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -186484,10 +163449,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -186513,8 +163474,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -186538,12 +163499,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -186553,9 +163514,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -186566,11 +163527,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -186616,6 +163572,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -186649,9 +163609,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.10.1+galaxy1",
"2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.10.1+galaxy1"
]
},
{
@@ -186674,10 +163634,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -186720,9 +163676,9 @@
"0.3.1",
"2.14.1+galaxy2",
"0.3.3",
- "0.3.0",
+ "0.1.07",
"0.0.11",
- "0.1.07"
+ "0.3.0"
]
},
{
@@ -186731,17 +163687,17 @@
"versions": [
"2.10.1+galaxy2",
"0.1.07",
- "0.0.22",
"0.1.06",
- "0.0.20",
- "0.0.19",
- "0.2.00",
- "0.0.14",
+ "0.1.04",
+ "0.1.00",
"0.1.08",
"0.2.01",
- "0.1.04",
- "0.1.01",
- "0.1.00"
+ "0.2.00",
+ "0.0.14",
+ "0.0.19",
+ "0.0.20",
+ "0.0.22",
+ "0.1.01"
]
},
{
@@ -186749,18 +163705,6 @@
"state": "exact",
"version": "2.10.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.1+galaxy2",
- "2.10.1+galaxy1",
- "2.14.1+galaxy2",
- "0.3.3",
- "2.14.1+galaxy1",
- "2.14.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -186806,6 +163750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -186859,10 +163807,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -186908,13 +163852,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "6.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -186959,6 +163896,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187011,10 +163952,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187057,11 +163994,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187106,6 +164038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187158,10 +164094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187204,11 +164136,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187253,6 +164180,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187305,10 +164236,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187351,11 +164278,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187400,6 +164322,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187452,10 +164378,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187498,11 +164420,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187547,6 +164464,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187599,10 +164520,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187645,11 +164562,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187694,6 +164606,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187746,10 +164662,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187792,11 +164704,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187841,6 +164748,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -187893,10 +164804,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -187939,11 +164846,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -187988,6 +164890,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -188040,10 +164946,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -188086,11 +164988,6 @@
"state": "exact",
"version": "1.2.13"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.13"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -188135,6 +165032,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -188188,10 +165089,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -188234,11 +165131,6 @@
"state": "exact",
"version": "0.2.7"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.2.7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -188284,6 +165176,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -188336,10 +165232,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -188380,10 +165272,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -188454,8 +165342,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 118,
- "visitors": 3273,
+ "visit_duration": 117,
+ "visitors": 3286,
"workflows": [
{
"creators": [],
@@ -188520,7 +165408,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nwolf_tutorial.zip?download=1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Illuminapairedend\"];\n 2[\"Unzip\"];\n 0 -->|output| 2;\n 3[\"FastQC\"];\n 1 -->|output| 3;\n 4[\"FASTQ Groomer\"];\n 1 -->|output| 4;\n 5[\"obigrep\"];\n 4 -->|output_file| 5;\n 6[\"Line/Word/Character count\"];\n 4 -->|output_file| 6;\n 7[\"Line/Word/Character count\"];\n 5 -->|output| 7;\n 8[\"NGSfilter\"];\n 5 -->|output| 8;\n 9[\"obiuniq\"];\n 8 -->|output| 9;\n 10[\"obiannotate\"];\n 9 -->|output| 10;\n 11[\"obistat\"];\n 10 -->|output| 11;\n 12[\"obigrep\"];\n 10 -->|output| 12;\n 13[\"obigrep\"];\n 12 -->|output| 13;\n 14[\"obiclean\"];\n 13 -->|output| 14;\n 15[\"NCBI BLAST+ blastn\"];\n 14 -->|output| 15;\n 16[\"Filter sequences by ID\"];\n 15 -->|output1| 16;\n 17[\"Filter sequences by ID\"];\n 15 -->|output1| 17;\n 14 -->|output| 17;\n 18[\"obitab\"];\n 16 -->|output_pos| 18;\n 19[\"obitab\"];\n 17 -->|output_pos| 19;\n 20[\"Join two Datasets\"];\n 19 -->|output| 20;\n 15 -->|output1| 20;\n 21[\"Join two Datasets\"];\n 20 -->|out_file1| 21;\n 18 -->|output| 21;\n 22[\"Cut\"];\n 21 -->|out_file1| 22;\n 23[\"Filter\"];\n 22 -->|out_file1| 23;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Workflow constructed from history 'Tuto Obitools'",
"outputs": [],
"parent_id": "ecology/Obitools-metabarcoding",
@@ -188733,10 +165621,10 @@
"topic_3697"
],
"edam_operation": [
+ "Taxonomic classification",
"Expression analysis",
- "Statistical calculation",
"Cross-assembly",
- "Taxonomic classification"
+ "Statistical calculation"
],
"edam_topic": [
"Whole genome sequencing",
@@ -188745,8 +165633,7 @@
"Microbial ecology"
],
"exact_supported_servers": [
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -188775,7 +165662,7 @@
"Run a series of tool to identify species in bacterial isolate sequencing data",
"Visualize the species abundance"
],
- "pageviews": 518,
+ "pageviews": 526,
"pub_date": "2024-03-04",
"questions": [
"What are the species in bacterial isolate sequencing data?"
@@ -188783,8 +165670,8 @@
"short_id": "T00423",
"short_tools": [
"kraken2",
- "upload1",
"est_abundance",
+ "upload1",
"recentrifuge"
],
"slides": false,
@@ -188796,11 +165683,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -188848,6 +165730,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -188903,10 +165789,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -188953,11 +165835,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -189002,6 +165879,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -189037,8 +165918,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.5+galaxy0",
- "2.6.1+galaxy0"
+ "2.6.1+galaxy0",
+ "2.5+galaxy0"
]
},
{
@@ -189061,10 +165942,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -189109,11 +165986,6 @@
"state": "exact",
"version": "2.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -189162,6 +166034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -189216,10 +166092,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -189253,8 +166125,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -189267,11 +166139,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -189317,6 +166184,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -189375,10 +166246,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -189421,11 +166288,6 @@
"state": "exact",
"version": "1.12.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.12.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -189435,8 +166297,8 @@
"state": "inexact",
"versions": [
"1.14.1+galaxy0",
- "1.14.0+galaxy0",
- "1.15.0+galaxy0"
+ "1.15.0+galaxy0",
+ "1.14.0+galaxy0"
]
},
{
@@ -189477,6 +166339,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -189529,10 +166395,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -189573,10 +166435,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -189631,8 +166489,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 221,
- "visitors": 368,
+ "visit_duration": 228,
+ "visitors": 374,
"workflows": [
{
"creators": [
@@ -189739,7 +166597,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Kraken2\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n 2 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n 54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n 2 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n 3[\"Bracken\"];\n 2 -->|report_output| 3;\n ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n 3 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n 3 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n 4[\"Recentrifuge\"];\n 2 -->|output| 4;\n b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n 4 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n 4 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n 4 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n 94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n 4 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Checking expected species and contamination in bacterial isolate",
"outputs": [
{
@@ -190331,8 +167189,8 @@
"short_id": "T00332",
"short_tools": [
"obisindicators",
- "obis_data",
- "tp_cut_tool"
+ "tp_cut_tool",
+ "obis_data"
],
"slides": false,
"slides_recordings": false,
@@ -190369,6 +167227,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -190424,10 +167286,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -190474,11 +167332,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -190523,6 +167376,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -190577,10 +167434,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -190628,11 +167481,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -190678,6 +167526,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -190736,10 +167588,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -190792,11 +167640,6 @@
"state": "exact",
"version": "9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -190849,6 +167692,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -190901,10 +167748,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -190946,10 +167789,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -190992,6 +167831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -191044,10 +167887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -191092,13 +167931,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.0.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -191144,6 +167976,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -191196,10 +168032,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -191242,11 +168074,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -191350,7 +168177,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"OBIS occurences\"];\n 1[\"Advanced Cut\"];\n 0 -->|output| 1;\n 2[\"Ocean biodiversity indicators\"];\n 1 -->|output| 2;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Marine Omics visualisation",
"outputs": [],
"parent_id": "ecology/obisindicators",
@@ -192069,22 +168896,6 @@
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
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"questions": [
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],
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+ "ecology_link_between_var",
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"tool_anonymization",
"regexColumn1",
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- "ecology_link_between_var",
"Remove beginning1",
- "ecology_stat_presence_abs",
- "ecology_homogeneity_normality",
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"ecology_beta_diversity",
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],
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]
},
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{
"name": "CoralSNP",
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"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -194017,11 +170627,6 @@
"url": "https://usegalaxy.eu",
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- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -194066,6 +170671,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -194118,10 +170727,6 @@
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{
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@@ -194162,10 +170767,6 @@
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{
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"state": "local"
@@ -194208,6 +170809,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -194363,6 +170959,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -194508,6 +171099,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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"state": "missing"
@@ -194653,6 +171239,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -194705,10 +171295,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -194751,11 +171337,6 @@
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{
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"state": "missing"
@@ -194798,6 +171379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -194850,10 +171435,6 @@
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@@ -194896,11 +171477,6 @@
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{
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@@ -194944,148 +171520,7 @@
"state": "missing"
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{
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- "state": "missing"
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- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -195140,10 +171575,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "missing"
@@ -195187,7 +171618,142 @@
"version": "0.0.0"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "missing"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.0.0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "0.0.0"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.0.0"
},
@@ -195233,6 +171799,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -195291,10 +171861,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -195343,15 +171909,6 @@
"state": "exact",
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},
- {
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- "state": "inexact",
- "versions": [
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- "1.0.1",
- "1.0.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -195419,8 +171976,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 161,
- "visitors": 1250,
+ "visit_duration": 160,
+ "visitors": 1262,
"workflows": [
{
"creators": [],
@@ -195483,7 +172040,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nReel_life_survey_fish_modif.tabular\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Spatial coordinates anonymization\"];\n 0 -->|output| 1;\n 2[\"Homoscedasticity and normality\"];\n 0 -->|output| 2;\n 3[\"Variables exploration\"];\n 0 -->|output| 3;\n 4[\"Presence-absence and abundance\"];\n 0 -->|output| 4;\n 5[\"Statistics on presence-absence\"];\n 0 -->|output| 5;\n 6[\"Local Contributions to Beta Diversity LCBD\"];\n 0 -->|output| 6;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Workflow 'Biodiversity data exploration tuto'",
"outputs": [
{
@@ -196110,7 +172667,7 @@
"Create timeseries and visualisation of the NDVI",
"Handle going form one interactive tool to another"
],
- "pageviews": 121,
+ "pageviews": 124,
"pub_date": "2024-01-24",
"questions": [
"What's the NDVI ?",
@@ -196118,8 +172675,8 @@
],
"short_id": "T00400",
"short_tools": [
- "interactive_tool_copernicus_notebook",
- "interactive_tool_holoviz"
+ "interactive_tool_holoviz",
+ "interactive_tool_copernicus_notebook"
],
"slides": false,
"slides_recordings": false,
@@ -196156,6 +172713,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -196211,10 +172772,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -196261,11 +172818,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -196310,6 +172862,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -196362,10 +172918,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -196406,10 +172958,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -196452,6 +173000,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -196504,10 +173056,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -196548,10 +173096,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -196606,8 +173150,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 91,
- "visitors": 100,
+ "visit_duration": 88,
+ "visitors": 103,
"workflows": [
{
"creators": [
@@ -196645,7 +173189,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Copernicus Data Space Ecosystem\"];\n 1[\"Holoviz\"];\n 0 -->|output_collection| 1;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "NDVI with OpenEO",
"outputs": [],
"parent_id": "ecology/ndvi_openeo",
@@ -196733,7 +173277,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Copernicus Data Space Ecosystem\"];\n 1[\"Holoviz\"];\n 0 -->|output_collection| 1;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "NDVI with OpenEO",
"outputs": [],
"parent_id": "ecology/ndvi_openeo",
@@ -196978,8 +173522,7 @@
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -197004,7 +173547,7 @@
"Calculating and visualizing biodiversity indicators",
"Comparing with in-situ data"
],
- "pageviews": 474,
+ "pageviews": 479,
"pub_date": "2023-04-13",
"questions": [
"How to get spectral and biodiversity indicators from remote sensing data ?",
@@ -197013,11 +173556,11 @@
"short_id": "T00333",
"short_tools": [
"srs_process_data",
+ "srs_diversity_maps",
"srs_global_indices",
"srs_pca",
"srs_spectral_indices",
- "srs_preprocess_s2",
- "srs_diversity_maps"
+ "srs_preprocess_s2"
],
"slides": false,
"slides_recordings": false,
@@ -197033,11 +173576,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": []
@@ -197064,6 +173602,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -197119,10 +173661,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -197169,11 +173707,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -197218,6 +173751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197270,10 +173807,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
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@@ -197316,11 +173849,6 @@
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- "version": "0.0.1"
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{
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"state": "missing"
@@ -197364,6 +173892,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197416,10 +173948,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -197462,11 +173990,6 @@
"state": "exact",
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- "state": "exact",
- "version": "0.0.1"
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{
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"state": "missing"
@@ -197510,6 +174033,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197562,10 +174089,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
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"state": "missing"
@@ -197608,11 +174131,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.1"
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{
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"state": "missing"
@@ -197655,6 +174173,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197707,10 +174229,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
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"state": "missing"
@@ -197753,11 +174271,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "0.0.1"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -197801,6 +174314,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197853,10 +174370,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -197899,11 +174412,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -197946,6 +174454,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -197998,10 +174510,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -198044,11 +174552,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -198104,8 +174607,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 91,
- "visitors": 373,
+ "visit_duration": 92,
+ "visitors": 378,
"workflows": [
{
"creators": [
@@ -198164,7 +174667,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Preprocess sentinel 2 data\"];\n 0 -->|output| 1;\n 2[\"Compute spectral indices\"];\n 1 -->|output_refl| 2;\n 3[\"Compute biodiversity indices\"];\n 1 -->|output_refl| 3;\n 4[\"Map diversity\"];\n 1 -->|output_refl| 4;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Sentinel 2 example",
"outputs": [
{
@@ -198462,22 +174965,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n owner: devteam\n revisions: f2e8552cf1d0\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_denovomap\n owner: iuc\n revisions: fdbcc560c691\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n owner: iuc\n revisions: 45db1ba16163\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n owner: iuc\n revisions: eded025438db\n tool_panel_section_label: RAD-seq\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json",
- "contributions": {
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- "reviewing": [
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- "shiltemann",
- "nsoranzo",
- "bgruening",
- "yvanlebras",
- "lecorguille",
- "bebatut",
- "willdurand",
- "njall"
- ]
- },
"contributors": [
{
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@@ -198497,195 +174984,14 @@
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"twitter": "Yvan2935",
"url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
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- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
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- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe"
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- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
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- "deNBI",
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "fnso2019",
- "elixir-europe"
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- "elixir_node": "fr",
- "email": "yvan.le-bras@mnhn.fr",
- "id": "yvanlebras",
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- "twitter": "Yvan2935",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
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- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
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- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
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- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/ecology/tutorials/de-novo-rad-seq",
"edam_operation": [
+ "Sequencing quality control",
"Sequence composition calculation",
"Data handling",
- "Statistical calculation",
- "Sequencing quality control"
+ "Statistical calculation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -198714,7 +175020,7 @@
"SNP calling from RAD sequencing data",
"Calculate population genomics statistics from RAD sequencing data"
],
- "pageviews": 3930,
+ "pageviews": 3942,
"pub_date": "2017-02-14",
"questions": [
"How to analyze RAD sequencing data without a reference genome for a population genomics study?"
@@ -198726,10 +175032,10 @@
],
"short_id": "T00128",
"short_tools": [
- "stacks_populations",
+ "stacks_procrad",
"stacks_denovomap",
- "fastqc",
- "stacks_procrad"
+ "stacks_populations",
+ "fastqc"
],
"slides": false,
"slides_recordings": false,
@@ -198787,6 +175093,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -198842,10 +175152,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -198892,11 +175198,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -198941,6 +175242,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -198966,8 +175271,8 @@
"state": "inexact",
"versions": [
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- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
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"state": "missing"
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- {
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{
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"state": "inexact",
@@ -199031,8 +175332,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
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@@ -199064,17 +175365,6 @@
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- "0.73+galaxy0",
- "0.72",
- "0.74+galaxy0",
- "0.74+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -199123,6 +175413,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -199175,10 +175469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -199222,10 +175512,6 @@
"state": "exact",
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},
- {
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -199271,162 +175557,7 @@
"state": "missing"
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{
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{
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+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
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"visit_duration": 127,
- "visitors": 2403,
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "de novo Rad Seq",
"outputs": [],
"parent_id": "ecology/de-novo-rad-seq",
@@ -199825,15 +176099,6 @@
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- "reviewing": [
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- "shiltemann"
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"contributors": [
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@@ -199841,68 +176106,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/Quickbeasts51429.json"
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- "uni-freiburg"
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- "gallantries",
- "erasmusmc"
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- "joined": "2017-09",
- "linkedin": "shiltemann",
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],
"dir": "topics/ecology/tutorials/x-array-map-plot",
@@ -199936,7 +176139,7 @@
"Learn about NetCDF xarray map plotting tool",
"Learn about visualizing the climate data using NetCDF xarray map plotting using the different kinds of projections and colormap options"
],
- "pageviews": 2414,
+ "pageviews": 2422,
"pub_date": "2022-10-26",
"questions": [
"What is xarray map plotting?",
@@ -199954,10 +176157,10 @@
],
"short_id": "T00136",
"short_tools": [
+ "graphicsmagick_image_montage",
"cdo_operations",
"xarray_mapplot",
"xarray_metadata_info",
- "graphicsmagick_image_montage",
"xarray_coords_info"
],
"slides": false,
@@ -200001,6 +176204,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -200056,10 +176263,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -200106,11 +176309,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -200155,6 +176353,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "exact",
@@ -200304,6 +176498,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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{
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"state": "missing"
@@ -200448,6 +176638,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -200500,10 +176694,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -200548,11 +176738,6 @@
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{
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"state": "missing"
@@ -200599,6 +176784,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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{
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@@ -200699,11 +176884,6 @@
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{
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"state": "missing"
@@ -200750,6 +176930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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{
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@@ -200848,14 +177028,6 @@
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{
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"state": "exact",
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"video_view": 0,
"visit_duration": 30,
- "visitors": 2064,
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@@ -200976,7 +177148,7 @@
],
"license": "MIT",
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Xarray_Map_Plotting_Workflow",
"outputs": [
{
@@ -201594,8 +177766,8 @@
"dir": "topics/ecology/tutorials/marine_omics_bgc",
"edam_operation": [
"Protein feature detection",
- "Genome annotation",
- "Sequence motif recognition"
+ "Sequence motif recognition",
+ "Genome annotation"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -201629,11 +177801,11 @@
],
"short_id": "T00450",
"short_tools": [
+ "sanntis_marine",
"SanntiS_marine",
- "prodigal",
"regex1",
"interproscan",
- "sanntis_marine"
+ "prodigal"
],
"slides": false,
"slides_recordings": false,
@@ -201664,6 +177836,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -201719,10 +177895,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -201769,11 +177941,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
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"url": "https://usegalaxy.no/",
@@ -201818,6 +177985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -201870,10 +178041,6 @@
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{
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@@ -201906,8 +178073,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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- "5.54-87.0+galaxy2"
+ "5.54-87.0+galaxy2",
+ "5.52-86.0+galaxy1"
]
},
{
@@ -201920,11 +178087,6 @@
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{
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"state": "exact",
@@ -201970,6 +178132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -202022,10 +178188,6 @@
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -202066,10 +178228,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -202112,6 +178270,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -202164,10 +178326,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -202209,10 +178367,6 @@
"state": "exact",
"version": "0.9.3.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -202256,6 +178410,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -202312,10 +178470,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -202363,11 +178517,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -202413,6 +178562,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -202465,10 +178618,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -202510,11 +178659,6 @@
"state": "exact",
"version": "2.6.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.6.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -202647,7 +178791,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nFasta nucelotide file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Prodigal Gene Predictor \"];\n 0 -->|output| 1;\n 351cf550-c05d-4bad-9394-fe9b45ef6298[\"Output\\nProtein fasta file\"];\n 1 --> 351cf550-c05d-4bad-9394-fe9b45ef6298;\n style 351cf550-c05d-4bad-9394-fe9b45ef6298 stroke:#2c3143,stroke-width:4px;\n 2[\"Sanntis: Build Genbank \"];\n 0 -->|output| 2;\n 1 -->|output_faa| 2;\n 1b9f0275-191a-4e90-b4b4-7b10475f4602[\"Output\\nGenbank file\"];\n 2 --> 1b9f0275-191a-4e90-b4b4-7b10475f4602;\n style 1b9f0275-191a-4e90-b4b4-7b10475f4602 stroke:#2c3143,stroke-width:4px;\n 3[\"Regex Find And Replace\"];\n 1 -->|output_faa| 3;\n e41e8fb9-c5f6-425f-a351-f8fa92f7821d[\"Output\\nClean protein fasta file\"];\n 3 --> e41e8fb9-c5f6-425f-a351-f8fa92f7821d;\n style e41e8fb9-c5f6-425f-a351-f8fa92f7821d stroke:#2c3143,stroke-width:4px;\n 4[\" InterProScan\"];\n 3 -->|out_file1| 4;\n 522b49db-7650-41e7-b888-01bb3cb1b451[\"Output\\nTabular file (.tsv)\"];\n 4 --> 522b49db-7650-41e7-b888-01bb3cb1b451;\n style 522b49db-7650-41e7-b888-01bb3cb1b451 stroke:#2c3143,stroke-width:4px;\n 5[\"Sanntis: identify biosynthetic gene clusters\"];\n 2 -->|output_sanntis_gb| 5;\n 4 -->|outfile_tsv| 5;\n c96c8c7e-0a50-4506-a144-9d941f50eb5e[\"Output\\n SMBGC Annotation\"];\n 5 --> c96c8c7e-0a50-4506-a144-9d941f50eb5e;\n style c96c8c7e-0a50-4506-a144-9d941f50eb5e stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Marine Omics identifying biosynthetic gene clusters",
"outputs": [
{
@@ -203038,22 +179182,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: 9ff72e942410\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_ab_index\n owner: ecology\n revisions: d0ee713d4758\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_autocor_acf\n owner: ecology\n revisions: b416a363a2d5\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_flight_curve\n owner: ecology\n revisions: fff507f00b2b\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_glmmpql\n owner: ecology\n revisions: f3e1b6d244a6\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_gls\n owner: ecology\n revisions: a79f5f0f17ad\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam_plot_trend\n owner: ecology\n revisions: 58ecd15e6836\n tool_panel_section_label: Species abundance\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n owner: galaxyp\n revisions: 209b7c5ee9d7\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n owner: iuc\n revisions: 9cec81e1b90e\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: csv_to_tabular\n owner: mnhn65mo\n revisions: b735ac78702b\n tool_panel_section_label: Ecology\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regionalgam\n owner: mnhn65mo\n revisions: 0e7066603eab\n tool_panel_section_label: Ecology\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_csv\n owner: mnhn65mo\n revisions: f1b7d0032530\n tool_panel_section_label: Ecology\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/regionalGAM/tutorial.json",
- "contributions": {
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- "claraurf",
- "emichn",
- "yvanlebras",
- "bebatut",
- "sbenateau"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "yvanlebras",
- "bgruening",
- "lecorguille"
- ]
- },
"contributors": [
{
"id": "claraurf",
@@ -203126,129 +179254,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/sbenateau/",
"twitter": "sbenateau",
"url": "https://training.galaxyproject.org/training-material/api/contributors/sbenateau.json"
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "pndb",
- "gallantries",
- "fairease",
- "fnso2019",
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "email": "yvan.le-bras@mnhn.fr",
- "id": "yvanlebras",
- "joined": "2017-09",
- "matrix": "yvanlebras:matrix.org",
- "name": "Yvan Le Bras",
- "orcid": "0000-0002-8504-068X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
- "twitter": "Yvan2935",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/ecology/tutorials/regionalGAM",
@@ -203284,30 +179289,30 @@
"Compute and visualize phenology of a species through the years",
"Compute temporal abundance trends"
],
- "pageviews": 390,
+ "pageviews": 392,
"pub_date": "2019-07-04",
"questions": [
"What are abundance and trends of a butterfly species?"
],
"short_id": "T00134",
"short_tools": [
- "tab2csv_R",
- "regexColumn1",
- "flight-curve",
- "tp_awk_tool",
- "Remove beginning1",
- "ggplot2_point",
- "Filter1",
+ "regionalgam_plot_trend",
"mergeCols1",
- "regionalgam_glmmpql",
+ "Filter1",
"regionalgam_gls",
+ "tab2csv_R",
"Count1",
- "regionalgam_plot_trend",
+ "tp_awk_tool",
+ "regexColumn1",
+ "regionalgam_autocor_acf",
+ "Remove beginning1",
+ "Paste1",
"regionalgam_ab_index",
"regionalgam_flight_curve",
+ "ggplot2_point",
"csv2tab_R",
- "regionalgam_autocor_acf",
- "Paste1"
+ "flight-curve",
+ "regionalgam_glmmpql"
],
"slides": false,
"slides_recordings": false,
@@ -203338,6 +179343,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -203393,10 +179402,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -203443,11 +179448,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -203492,6 +179492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -203544,10 +179548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -203588,10 +179588,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -203634,6 +179630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -203686,10 +179686,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -203730,10 +179726,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -203776,6 +179768,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -203828,10 +179824,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -203872,10 +179864,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -203918,6 +179906,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -203970,10 +179962,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -204014,10 +180002,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -204060,6 +180044,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -204112,10 +180100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -204156,10 +180140,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -204202,6 +180182,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -204258,10 +180242,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -204311,11 +180291,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -204365,6 +180340,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -204417,10 +180396,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -204464,11 +180439,6 @@
"state": "exact",
"version": "1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -204512,6 +180482,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -204564,10 +180538,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -204611,11 +180581,6 @@
"state": "exact",
"version": "1.5"
},
- {
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@@ -205417,6 +181353,10 @@
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@@ -205473,10 +181413,6 @@
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@@ -205525,18 +181461,6 @@
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@@ -205556,10 +181480,10 @@
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"3.4.0+galaxy1",
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+ "3.4.0+galaxy0",
"3.3.5+galaxy1",
"3.3.5+galaxy0",
- "3.4.0+galaxy0"
+ "3.3.5+galaxy2"
]
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{
@@ -205592,6 +181516,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -205645,10 +181573,6 @@
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@@ -205737,6 +181657,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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@@ -205789,10 +181713,6 @@
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@@ -205834,11 +181754,6 @@
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@@ -205881,6 +181796,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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@@ -205933,10 +181852,6 @@
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@@ -205978,10 +181893,6 @@
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{
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@@ -206050,8 +181961,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 205,
- "visitors": 284,
+ "visit_duration": 202,
+ "visitors": 286,
"workflows": [
{
"creators": [],
@@ -206118,7 +182029,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAbundance index file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Filter\"];\n 0 -->|output| 1;\n 2[\"Filter\"];\n 0 -->|output| 2;\n 3[\"Filter\"];\n 0 -->|output| 3;\n 4[\"Filter\"];\n 0 -->|output| 4;\n 5[\"Filter\"];\n 0 -->|output| 5;\n 6[\"Paste\"];\n 1 -->|out_file1| 6;\n 2 -->|out_file1| 6;\n 7[\"Paste\"];\n 3 -->|out_file1| 7;\n 4 -->|out_file1| 7;\n 8[\"Paste\"];\n 6 -->|out_file1| 8;\n 7 -->|out_file1| 8;\n 9[\"Paste\"];\n 8 -->|out_file1| 9;\n 5 -->|out_file1| 9;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Abundance Index \"stacked\" Visualization Creation",
"outputs": [],
"parent_id": "ecology/regionalGAM",
@@ -206209,7 +182120,7 @@
],
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Phenology \"stacked\" Visualization Creation",
"outputs": [],
"parent_id": "ecology/regionalGAM",
@@ -206305,7 +182216,7 @@
],
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Tutorial regionalGAM Complete Multispecies",
"outputs": [],
"parent_id": "ecology/regionalGAM",
@@ -206415,7 +182326,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Regional GAM Workflow",
"outputs": [
{
@@ -207063,8 +182974,7 @@
"edam_operation": [],
"edam_topic": [],
"exact_supported_servers": [
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- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -207108,11 +183018,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": []
@@ -207139,6 +183044,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -207194,10 +183103,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -207244,11 +183149,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -207293,6 +183193,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -207345,10 +183249,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -207389,10 +183289,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -207538,18 +183434,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: glimmer_gbk_to_orf\n owner: bgruening\n revisions: '04861c9bbf45'\n tool_panel_section_label: Ecology\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: repeat_masker\n owner: bgruening\n revisions: 39b40a9a6296\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n owner: devteam\n revisions: d6694932c5e0\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n owner: galaxyp\n revisions: ae8c4b2488e7\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 602fb8e63aa7\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n owner: iuc\n revisions: 2bba2ff070d9\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteinortho\n owner: iuc\n revisions: 4850f0d15f01\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 830961c48e42\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clipkit\n owner: padge\n revisions: '770695339600'\n tool_panel_section_label: Phylogenetics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: phykit\n owner: padge\n revisions: 1ac6ee298657\n tool_panel_section_label: Ecology\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json",
- "contributions": {
- "authorship": [
- "roncoronimiguel",
- "brigidagallone"
- ],
- "reviewing": [
- "hexylena",
- "roncoronimiguel",
- "bebatut",
- "shiltemann"
- ]
- },
"contributors": [
{
"email": "miguel.roncoroni@elixir-belgium.org",
@@ -207566,115 +183450,19 @@
"orcid": "0000-0003-3045-5949",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/brigidagallone/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/brigidagallone.json"
- },
- {
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "email": "miguel.roncoroni@elixir-belgium.org",
- "id": "roncoronimiguel",
- "joined": "2021-08",
- "name": "Miguel Roncoroni",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/roncoronimiguel/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/roncoronimiguel.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/ecology/tutorials/phylogeny-data-prep",
"edam_operation": [
- "Sequence clustering",
+ "Genetic variation analysis",
"Multiple sequence alignment",
+ "Sequence clustering",
"Genome assembly",
- "Sequence assembly validation",
- "Genetic variation analysis",
- "Sequence analysis",
"Genome annotation",
+ "Sequence assembly validation",
"Transcriptome assembly",
- "Scaffolding"
+ "Scaffolding",
+ "Sequence analysis"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -207704,7 +183492,7 @@
"Find a set of common proteins across the samples (orthologs)",
"Align orthologs across samples"
],
- "pageviews": 2237,
+ "pageviews": 2243,
"pub_date": "2022-10-21",
"questions": [
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@@ -207721,19 +183509,19 @@
],
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- "phykit_alignment_based",
- "clipkit",
- "proteinortho_grab_proteins",
- "proteinortho",
- "tp_replace_in_line",
- "Filter1",
- "regex1",
- "clustalw",
"funannotate_predict",
+ "Filter1",
+ "proteinortho_grab_proteins",
+ "collapse_dataset",
+ "phykit_alignment_based",
"glimmer_gbk_to_orf",
"busco",
- "collapse_dataset"
+ "repeatmasker_wrapper",
+ "proteinortho",
+ "regex1",
+ "clipkit",
+ "tp_replace_in_line",
+ "clustalw"
],
"slides": false,
"slides_recordings": false,
@@ -207770,6 +183558,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -207825,10 +183617,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -207875,11 +183663,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -207924,6 +183707,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -207976,10 +183763,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -208020,10 +183803,6 @@
"server": "https://usegalaxy.eu",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -208066,6 +183845,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -208118,10 +183901,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
- },
{
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"state": "missing"
@@ -208163,10 +183942,6 @@
"server": "https://usegalaxy.eu",
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- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
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"state": "missing"
@@ -208209,6 +183984,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -208261,10 +184040,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
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"state": "missing"
@@ -208310,11 +184085,6 @@
"state": "exact",
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},
- {
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- "state": "exact",
- "version": "4.1.2-p1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -208363,6 +184133,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -208417,10 +184191,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
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"state": "inexact",
@@ -208467,11 +184237,6 @@
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- "version": "1.1.2"
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{
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"state": "exact",
@@ -208517,6 +184282,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -208571,10 +184340,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -208620,11 +184385,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -208670,6 +184430,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -208726,10 +184490,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -208778,11 +184538,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -208830,6 +184585,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -208862,10 +184621,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -208888,10 +184647,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -208937,23 +184692,6 @@
"state": "exact",
"version": "4.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
- "5.2.2+galaxy2",
- "5.3.1+galaxy0",
- "5.3.2+galaxy0",
- "5.5.0+galaxy0",
- "5.2.2+galaxy0",
- "5.7.1+galaxy0",
- "5.8.0+galaxy0",
- "5.4.5+galaxy0",
- "5.2.2+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -208999,6 +184737,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209051,10 +184793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -209100,11 +184838,6 @@
"state": "exact",
"version": "1.8.9+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.9+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -209114,10 +184847,10 @@
"state": "inexact",
"versions": [
"1.8.15+galaxy5",
+ "1.8.15+galaxy3",
"1.8.15+galaxy0",
- "1.8.15+galaxy1",
"1.8.15+galaxy4",
- "1.8.15+galaxy3"
+ "1.8.15+galaxy1"
]
},
{
@@ -209155,6 +184888,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209207,10 +184944,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -209256,10 +184989,6 @@
"state": "exact",
"version": "6.0.14+galaxy2.9.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -209303,6 +185032,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209356,10 +185089,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -209405,10 +185134,6 @@
"state": "exact",
"version": "6.0.14+galaxy2.9.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -209452,6 +185177,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209508,10 +185237,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -209561,14 +185286,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -209614,6 +185331,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209666,10 +185387,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -209711,10 +185428,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -209758,6 +185471,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -209810,10 +185527,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -209855,10 +185568,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -209922,8 +185631,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 169,
- "visitors": 1643,
+ "visit_duration": 168,
+ "visitors": 1649,
"workflows": [
{
"creators": [
@@ -209993,7 +185702,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput genomes as collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Replace Text\"];\n 0 -->|output| 1;\n 6a2d3fcd-b557-4440-910d-b4c537feef20[\"Output\\nheaders_shortened\"];\n 1 --> 6a2d3fcd-b557-4440-910d-b4c537feef20;\n style 6a2d3fcd-b557-4440-910d-b4c537feef20 stroke:#2c3143,stroke-width:4px;\n 2[\"RepeatMasker\"];\n 1 -->|outfile| 2;\n 1db6607a-343a-4a61-9a3b-43101eb8223b[\"Output\\nrepeat_masked\"];\n 2 --> 1db6607a-343a-4a61-9a3b-43101eb8223b;\n style 1db6607a-343a-4a61-9a3b-43101eb8223b stroke:#2c3143,stroke-width:4px;\n 3[\"Funannotate predict annotation\"];\n 2 -->|output_masked_genome| 3;\n 642c1c09-82f4-4ef4-bd53-d14a583044e2[\"Output\\nfunannotate_predicted_proteins\"];\n 3 --> 642c1c09-82f4-4ef4-bd53-d14a583044e2;\n style 642c1c09-82f4-4ef4-bd53-d14a583044e2 stroke:#2c3143,stroke-width:4px;\n 4[\"Extract ORF\"];\n 3 -->|annot_gbk| 4;\n 07fb8c04-990e-4bc7-b607-9c4161b4786d[\"Output\\nextracted_ORFs\"];\n 4 --> 07fb8c04-990e-4bc7-b607-9c4161b4786d;\n style 07fb8c04-990e-4bc7-b607-9c4161b4786d stroke:#2c3143,stroke-width:4px;\n 5[\"Regex Find And Replace\"];\n 4 -->|aa_output| 5;\n 8dc378a8-d485-42df-8322-6cf8230257a0[\"Output\\nsample_names_to_headers\"];\n 5 --> 8dc378a8-d485-42df-8322-6cf8230257a0;\n style 8dc378a8-d485-42df-8322-6cf8230257a0 stroke:#2c3143,stroke-width:4px;\n 6[\"Collapse Collection\"];\n 5 -->|out_file1| 6;\n e9a55459-4a2c-4238-8494-e99ec67307ea[\"Output\\nproteomes_to_one_file\"];\n 6 --> e9a55459-4a2c-4238-8494-e99ec67307ea;\n style e9a55459-4a2c-4238-8494-e99ec67307ea stroke:#2c3143,stroke-width:4px;\n 7[\"Proteinortho\"];\n 5 -->|out_file1| 7;\n ee688b7a-2a9e-4480-a27a-db8cf795b635[\"Output\\nProteinortho on input dataset(s): orthology-groups\"];\n 7 --> ee688b7a-2a9e-4480-a27a-db8cf795b635;\n style ee688b7a-2a9e-4480-a27a-db8cf795b635 stroke:#2c3143,stroke-width:4px;\n 8[\"Busco\"];\n 5 -->|out_file1| 8;\n 9[\"Filter\"];\n 7 -->|proteinortho| 9;\n 10[\"Proteinortho grab proteins\"];\n 6 -->|output| 10;\n 9 -->|out_file1| 10;\n 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2[\"Output\\nProteinortho_extract_by_orthogroup\"];\n 10 --> 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2;\n style 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2 stroke:#2c3143,stroke-width:4px;\n 11[\"Regex Find And Replace\"];\n 10 -->|listproteinorthograbproteins| 11;\n b072d32e-f725-4833-af0b-74f4df526d9a[\"Output\\nfasta_header_cleaned\"];\n 11 --> b072d32e-f725-4833-af0b-74f4df526d9a;\n style b072d32e-f725-4833-af0b-74f4df526d9a stroke:#2c3143,stroke-width:4px;\n 12[\"ClustalW\"];\n 11 -->|out_file1| 12;\n f704b4b2-5214-4393-8a85-6274bda27c8c[\"Output\\nClustalW on input dataset(s): clustal\"];\n 12 --> f704b4b2-5214-4393-8a85-6274bda27c8c;\n style f704b4b2-5214-4393-8a85-6274bda27c8c stroke:#2c3143,stroke-width:4px;\n 13[\"ClipKIT. Alignment trimming software for phylogenetics.\"];\n 12 -->|output| 13;\n 37092981-191a-4413-8f60-51802dd95f9c[\"Output\\nTrimmed alignment.\"];\n 13 --> 37092981-191a-4413-8f60-51802dd95f9c;\n style 37092981-191a-4413-8f60-51802dd95f9c stroke:#2c3143,stroke-width:4px;\n 14[\"PhyKit - Alignment-based functions\"];\n 13 -->|trimmed_output| 14;\n 09ad25e3-cd68-4fb4-9c57-3e79212b8e01[\"Output\\nConcatenated fasta alignment file\"];\n 14 --> 09ad25e3-cd68-4fb4-9c57-3e79212b8e01;\n style 09ad25e3-cd68-4fb4-9c57-3e79212b8e01 stroke:#2c3143,stroke-width:4px;\n 1d546e4c-7e3c-499d-870c-4846feb7a46d[\"Output\\nA partition file ready for input into RAxML or IQ-tree\"];\n 14 --> 1d546e4c-7e3c-499d-870c-4846feb7a46d;\n style 1d546e4c-7e3c-499d-870c-4846feb7a46d stroke:#2c3143,stroke-width:4px;\n 26846814-d43a-4ce7-9f26-cfb70f184dce[\"Output\\nAn occupancy file that summarizes the taxon occupancy per sequence\"];\n 14 --> 26846814-d43a-4ce7-9f26-cfb70f184dce;\n style 26846814-d43a-4ce7-9f26-cfb70f184dce stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "preparing genomic data for phylogeny recostruction (GTN)",
"outputs": [
{
@@ -211236,7 +186945,7 @@
"Learning about Clara clustering algorithm (PAM for large datasets)",
"Create an ecoregionalization map"
],
- "pageviews": 84,
+ "pageviews": 86,
"pub_date": "2024-09-16",
"questions": [
"How to use the ecoregionalization workflow?",
@@ -211244,18 +186953,18 @@
],
"short_id": "T00455",
"short_tools": [
- "ecoregion_GeoNearestNeighbor",
+ "ecoregion_taxa_seeker",
+ "ecoregion_clara_cluster",
+ "mergeCols1",
"ecoregion_eco_map",
+ "ecoregion_brt_analysis",
+ "ecoregion_cluster_estimate",
"unzip",
"regexColumn1",
- "tp_cut_tool",
- "ecoregion_brt_analysis",
- "ecoregion_taxa_seeker",
- "mergeCols1",
"filter_tabular",
- "ecoregion_cluster_estimate",
- "interactive_tool_jupyter_notebook",
- "ecoregion_clara_cluster"
+ "ecoregion_GeoNearestNeighbor",
+ "tp_cut_tool",
+ "interactive_tool_jupyter_notebook"
],
"slides": false,
"slides_recordings": false,
@@ -211292,6 +187001,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -211347,10 +187060,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -211397,11 +187106,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -211446,6 +187150,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -211498,10 +187206,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -211542,10 +187246,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -211588,6 +187288,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -211646,10 +187350,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -211699,11 +187399,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -211751,6 +187446,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -211803,10 +187502,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -211850,13 +187545,6 @@
"state": "exact",
"version": "1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -211900,6 +187588,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -211952,10 +187644,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -211998,11 +187686,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212045,6 +187728,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212097,10 +187784,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -212143,11 +187826,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212190,6 +187868,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212242,10 +187924,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -212288,11 +187966,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212335,6 +188008,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212387,10 +188064,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -212433,11 +188106,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212480,6 +188148,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212532,10 +188204,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -212577,10 +188245,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212623,6 +188287,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212675,10 +188343,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -212721,11 +188385,6 @@
"state": "exact",
"version": "0.1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -212768,6 +188427,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212824,10 +188487,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -212875,11 +188534,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -212925,6 +188579,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -212980,10 +188638,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -213029,11 +188683,6 @@
"state": "exact",
"version": "6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -213080,6 +188729,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -213134,10 +188787,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -213184,10 +188833,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -213259,7 +188904,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 226,
- "visitors": 53,
+ "visitors": 54,
"workflows": [
{
"creators": [
@@ -213276,7 +188921,7 @@
"report": null,
"subworkflows": false
},
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"history": [
{
"hash": "106094184ea15924f444a0b076b0afecd065494a",
@@ -213370,8 +189015,8 @@
}
],
"license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Advanced Cut\"];\n 0 -->|output| 3;\n 4[\"Column Regex Find And Replace\"];\n 3 -->|output| 4;\n 5[\"Column Regex Find And Replace\"];\n 4 -->|out_file1| 5;\n 6[\"Column Regex Find And Replace\"];\n 5 -->|out_file1| 6;\n 7[\"Column Regex Find And Replace\"];\n 6 -->|out_file1| 7;\n 8[\"Filter Tabular\"];\n 7 -->|out_file1| 8;\n 9[\"Column Regex Find And Replace\"];\n 8 -->|output| 9;\n 10[\"Column Regex Find And Replace\"];\n 9 -->|out_file1| 10;\n 11[\"Column Regex Find And Replace\"];\n 10 -->|out_file1| 11;\n 12[\"Column Regex Find And Replace\"];\n 11 -->|out_file1| 12;\n 13[\"Column Regex Find And Replace\"];\n 12 -->|out_file1| 13;\n 14[\"Merge Columns\"];\n 13 -->|out_file1| 14;\n 15[\"Advanced Cut\"];\n 14 -->|out_file1| 15;\n 16[\"Interactive JupyTool and notebook\"];\n 1 -->|output| 16;\n 15 -->|output| 16;\n 2cd6bd16-2518-46e3-ac1c-dbdf410f267f[\"Output\\nocc_out\"];\n 16 --> 2cd6bd16-2518-46e3-ac1c-dbdf410f267f;\n style 2cd6bd16-2518-46e3-ac1c-dbdf410f267f stroke:#2c3143,stroke-width:4px;\n 17[\"GeoNearestNeighbor\"];\n 2 -->|output| 17;\n 16 -->|output_dataset| 17;\n e22ea914-e4ff-43b8-9693-876c1044fa1c[\"Output\\nocc_env_out\"];\n 17 --> e22ea914-e4ff-43b8-9693-876c1044fa1c;\n style e22ea914-e4ff-43b8-9693-876c1044fa1c stroke:#2c3143,stroke-width:4px;\n 88c5c930-58bb-43c1-936b-68adec159025[\"Output\\ninfo_out\"];\n 17 --> 88c5c930-58bb-43c1-936b-68adec159025;\n style 88c5c930-58bb-43c1-936b-68adec159025 stroke:#2c3143,stroke-width:4px;\n 18[\"BRT tool prediction\"];\n 2 -->|output| 18;\n 17 -->|occ_env_out| 18;\n 34781dec-6527-4673-9560-b9e3943a19be[\"Output\\ncoll_pred\"];\n 18 --> 34781dec-6527-4673-9560-b9e3943a19be;\n style 34781dec-6527-4673-9560-b9e3943a19be stroke:#2c3143,stroke-width:4px;\n bce3b345-7b59-4dc7-add9-17385191263f[\"Output\\ncoll_val\"];\n 18 --> bce3b345-7b59-4dc7-add9-17385191263f;\n style bce3b345-7b59-4dc7-add9-17385191263f stroke:#2c3143,stroke-width:4px;\n 3248bab0-db4c-4a7e-9abc-d507d953f6b7[\"Output\\ncoll_distri\"];\n 18 --> 3248bab0-db4c-4a7e-9abc-d507d953f6b7;\n style 3248bab0-db4c-4a7e-9abc-d507d953f6b7 stroke:#2c3143,stroke-width:4px;\n 5e95d85f-5001-46ed-aa2a-7dbb7ba84184[\"Output\\ncoll_plots\"];\n 18 --> 5e95d85f-5001-46ed-aa2a-7dbb7ba84184;\n style 5e95d85f-5001-46ed-aa2a-7dbb7ba84184 stroke:#2c3143,stroke-width:4px;\n 19[\"TaxaSeeker\"];\n 2 -->|output| 19;\n 17 -->|occ_env_out| 19;\n 18 -->|outputpred| 19;\n a161c36b-e5ca-43e2-b6ec-c8e4bf530993[\"Output\\nsummary\"];\n 19 --> a161c36b-e5ca-43e2-b6ec-c8e4bf530993;\n style a161c36b-e5ca-43e2-b6ec-c8e4bf530993 stroke:#2c3143,stroke-width:4px;\n 50d49830-a624-425e-8476-026358c44f04[\"Output\\ntaxa\"];\n 19 --> 50d49830-a624-425e-8476-026358c44f04;\n style 50d49830-a624-425e-8476-026358c44f04 stroke:#2c3143,stroke-width:4px;\n 1c833e40-98b2-42f3-a6d5-5a9d27d9ea92[\"Output\\ntaxa_clean\"];\n 19 --> 1c833e40-98b2-42f3-a6d5-5a9d27d9ea92;\n style 1c833e40-98b2-42f3-a6d5-5a9d27d9ea92 stroke:#2c3143,stroke-width:4px;\n 20[\"ClusterEstimate\"];\n 2 -->|output| 20;\n 18 -->|outputpred| 20;\n 19 -->|output2| 20;\n f4da174e-cd04-42d4-bbf1-38d270e13c18[\"Output\\nSIH_index\"];\n 20 --> f4da174e-cd04-42d4-bbf1-38d270e13c18;\n style f4da174e-cd04-42d4-bbf1-38d270e13c18 stroke:#2c3143,stroke-width:4px;\n 409d3120-a20d-4922-9989-431e8ab3ea3a[\"Output\\ndata_to_clus\"];\n 20 --> 409d3120-a20d-4922-9989-431e8ab3ea3a;\n style 409d3120-a20d-4922-9989-431e8ab3ea3a stroke:#2c3143,stroke-width:4px;\n d27a51e8-5d98-4958-a191-34fd938204f9[\"Output\\ndatabio_table\"];\n 20 --> d27a51e8-5d98-4958-a191-34fd938204f9;\n style d27a51e8-5d98-4958-a191-34fd938204f9 stroke:#2c3143,stroke-width:4px;\n 21[\"ClaraClust\"];\n 2 -->|output| 21;\n 20 -->|output3| 21;\n 20 -->|output2| 21;\n 06e63c29-8df0-42f1-afe2-c694d2f68e30[\"Output\\nSIH_plot\"];\n 21 --> 06e63c29-8df0-42f1-afe2-c694d2f68e30;\n style 06e63c29-8df0-42f1-afe2-c694d2f68e30 stroke:#2c3143,stroke-width:4px;\n 2dcc97ea-465a-4305-931c-7fee8e292adc[\"Output\\ncluster_points\"];\n 21 --> 2dcc97ea-465a-4305-931c-7fee8e292adc;\n style 2dcc97ea-465a-4305-931c-7fee8e292adc stroke:#2c3143,stroke-width:4px;\n 8f9568e8-f8fe-4059-b3f6-4d0f5bfcafdf[\"Output\\ncluster_info\"];\n 21 --> 8f9568e8-f8fe-4059-b3f6-4d0f5bfcafdf;\n style 8f9568e8-f8fe-4059-b3f6-4d0f5bfcafdf stroke:#2c3143,stroke-width:4px;\n 22[\"EcoMap\"];\n 21 -->|output2| 22;\n 772cd5d6-edfb-4d55-9dcc-b52354c7ce62[\"Output\\neco_map\"];\n 22 --> 772cd5d6-edfb-4d55-9dcc-b52354c7ce62;\n style 772cd5d6-edfb-4d55-9dcc-b52354c7ce62 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Advanced Cut\"];\n 0 -->|output| 3;\n 4[\"Column Regex Find And Replace\"];\n 3 -->|output| 4;\n 5[\"Column Regex Find And Replace\"];\n 4 -->|out_file1| 5;\n 6[\"Column Regex Find And Replace\"];\n 5 -->|out_file1| 6;\n 7[\"Column Regex Find And Replace\"];\n 6 -->|out_file1| 7;\n 8[\"Filter Tabular\"];\n 7 -->|out_file1| 8;\n 9[\"Column Regex Find And Replace\"];\n 8 -->|output| 9;\n 10[\"Column Regex Find And Replace\"];\n 9 -->|out_file1| 10;\n 11[\"Column Regex Find And Replace\"];\n 10 -->|out_file1| 11;\n 12[\"Column Regex Find And Replace\"];\n 11 -->|out_file1| 12;\n 13[\"Column Regex Find And Replace\"];\n 12 -->|out_file1| 13;\n 14[\"Merge Columns\"];\n 13 -->|out_file1| 14;\n 15[\"Advanced Cut\"];\n 14 -->|out_file1| 15;\n 16[\"Interactive JupyTool and notebook\"];\n 1 -->|output| 16;\n 15 -->|output| 16;\n 6c76e49d-2fa8-4da4-b3a9-9c3ffefa2ef6[\"Output\\nocc_out\"];\n 16 --> 6c76e49d-2fa8-4da4-b3a9-9c3ffefa2ef6;\n style 6c76e49d-2fa8-4da4-b3a9-9c3ffefa2ef6 stroke:#2c3143,stroke-width:4px;\n 17[\"GeoNearestNeighbor\"];\n 2 -->|output| 17;\n 16 -->|output_dataset| 17;\n f2939883-6a4b-456b-aded-82d1a0d9da8f[\"Output\\nocc_env_out\"];\n 17 --> f2939883-6a4b-456b-aded-82d1a0d9da8f;\n style f2939883-6a4b-456b-aded-82d1a0d9da8f stroke:#2c3143,stroke-width:4px;\n 265a4dec-87b1-4c52-bc72-183f598f7b63[\"Output\\ninfo_out\"];\n 17 --> 265a4dec-87b1-4c52-bc72-183f598f7b63;\n style 265a4dec-87b1-4c52-bc72-183f598f7b63 stroke:#2c3143,stroke-width:4px;\n 18[\"BRT tool prediction\"];\n 2 -->|output| 18;\n 17 -->|occ_env_out| 18;\n 79fa2792-881f-4f5a-be58-0293170f904e[\"Output\\ncoll_pred\"];\n 18 --> 79fa2792-881f-4f5a-be58-0293170f904e;\n style 79fa2792-881f-4f5a-be58-0293170f904e stroke:#2c3143,stroke-width:4px;\n 1722181d-18fe-45ee-9f0a-95b8f72ad6e2[\"Output\\ncoll_val\"];\n 18 --> 1722181d-18fe-45ee-9f0a-95b8f72ad6e2;\n style 1722181d-18fe-45ee-9f0a-95b8f72ad6e2 stroke:#2c3143,stroke-width:4px;\n f67d3b6f-92ad-4e04-8d6a-74d8456eed38[\"Output\\ncoll_distri\"];\n 18 --> f67d3b6f-92ad-4e04-8d6a-74d8456eed38;\n style f67d3b6f-92ad-4e04-8d6a-74d8456eed38 stroke:#2c3143,stroke-width:4px;\n a8a2707d-0f59-456c-bfec-d815daaae2c4[\"Output\\ncoll_plots\"];\n 18 --> a8a2707d-0f59-456c-bfec-d815daaae2c4;\n style a8a2707d-0f59-456c-bfec-d815daaae2c4 stroke:#2c3143,stroke-width:4px;\n 19[\"TaxaSeeker\"];\n 2 -->|output| 19;\n 17 -->|occ_env_out| 19;\n 18 -->|outputpred| 19;\n 1429e84c-e012-4596-a893-900b283cf0ea[\"Output\\nsummary\"];\n 19 --> 1429e84c-e012-4596-a893-900b283cf0ea;\n style 1429e84c-e012-4596-a893-900b283cf0ea stroke:#2c3143,stroke-width:4px;\n cfad7c38-abcb-4f0d-8e13-d06c73f9d6ea[\"Output\\ntaxa\"];\n 19 --> cfad7c38-abcb-4f0d-8e13-d06c73f9d6ea;\n style cfad7c38-abcb-4f0d-8e13-d06c73f9d6ea stroke:#2c3143,stroke-width:4px;\n d6e34653-b42c-472c-9013-fea030efe2d5[\"Output\\ntaxa_clean\"];\n 19 --> d6e34653-b42c-472c-9013-fea030efe2d5;\n style d6e34653-b42c-472c-9013-fea030efe2d5 stroke:#2c3143,stroke-width:4px;\n 20[\"ClusterEstimate\"];\n 2 -->|output| 20;\n 18 -->|outputpred| 20;\n 19 -->|output2| 20;\n 3a7776a6-c9df-4334-89a5-1882aa02ef67[\"Output\\nSIH_index\"];\n 20 --> 3a7776a6-c9df-4334-89a5-1882aa02ef67;\n style 3a7776a6-c9df-4334-89a5-1882aa02ef67 stroke:#2c3143,stroke-width:4px;\n 8dcb4453-0010-43cd-b7ae-d362c7d91809[\"Output\\ndata_to_clus\"];\n 20 --> 8dcb4453-0010-43cd-b7ae-d362c7d91809;\n style 8dcb4453-0010-43cd-b7ae-d362c7d91809 stroke:#2c3143,stroke-width:4px;\n 37324d39-bdf0-47c8-b3e2-09744ecfe905[\"Output\\ndatabio_table\"];\n 20 --> 37324d39-bdf0-47c8-b3e2-09744ecfe905;\n style 37324d39-bdf0-47c8-b3e2-09744ecfe905 stroke:#2c3143,stroke-width:4px;\n 21[\"ClaraClust\"];\n 2 -->|output| 21;\n 20 -->|output3| 21;\n 20 -->|output2| 21;\n 626693c4-5f50-4280-bd3c-27f339924290[\"Output\\nSIH_plot\"];\n 21 --> 626693c4-5f50-4280-bd3c-27f339924290;\n style 626693c4-5f50-4280-bd3c-27f339924290 stroke:#2c3143,stroke-width:4px;\n 0e65a0db-1607-473e-a904-e6f91ed9123c[\"Output\\ncluster_points\"];\n 21 --> 0e65a0db-1607-473e-a904-e6f91ed9123c;\n style 0e65a0db-1607-473e-a904-e6f91ed9123c stroke:#2c3143,stroke-width:4px;\n 3b126e94-1754-434f-95d0-80c59e64e57c[\"Output\\ncluster_info\"];\n 21 --> 3b126e94-1754-434f-95d0-80c59e64e57c;\n style 3b126e94-1754-434f-95d0-80c59e64e57c stroke:#2c3143,stroke-width:4px;\n 22[\"EcoMap\"];\n 21 -->|output2| 22;\n 5608bede-e9a3-41cb-b411-04331cc3339b[\"Output\\neco_map\"];\n 22 --> 5608bede-e9a3-41cb-b411-04331cc3339b;\n style 5608bede-e9a3-41cb-b411-04331cc3339b stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Ecoregionalization workflow",
"outputs": [
{
@@ -213434,7 +189079,7 @@
{
"label": "occ_out",
"output_name": "output_dataset",
- "uuid": "2cd6bd16-2518-46e3-ac1c-dbdf410f267f"
+ "uuid": "6c76e49d-2fa8-4da4-b3a9-9c3ffefa2ef6"
}
]
},
@@ -213496,12 +189141,12 @@
{
"label": "occ_env_out",
"output_name": "occ_env_out",
- "uuid": "e22ea914-e4ff-43b8-9693-876c1044fa1c"
+ "uuid": "f2939883-6a4b-456b-aded-82d1a0d9da8f"
},
{
"label": "info_out",
"output_name": "info_out",
- "uuid": "88c5c930-58bb-43c1-936b-68adec159025"
+ "uuid": "265a4dec-87b1-4c52-bc72-183f598f7b63"
}
]
},
@@ -213562,22 +189207,22 @@
{
"label": "coll_pred",
"output_name": "outputpred",
- "uuid": "34781dec-6527-4673-9560-b9e3943a19be"
+ "uuid": "79fa2792-881f-4f5a-be58-0293170f904e"
},
{
"label": "coll_val",
"output_name": "outputval",
- "uuid": "bce3b345-7b59-4dc7-add9-17385191263f"
+ "uuid": "1722181d-18fe-45ee-9f0a-95b8f72ad6e2"
},
{
"label": "coll_distri",
"output_name": "outputspdistri",
- "uuid": "3248bab0-db4c-4a7e-9abc-d507d953f6b7"
+ "uuid": "f67d3b6f-92ad-4e04-8d6a-74d8456eed38"
},
{
"label": "coll_plots",
"output_name": "outputplots",
- "uuid": "5e95d85f-5001-46ed-aa2a-7dbb7ba84184"
+ "uuid": "a8a2707d-0f59-456c-bfec-d815daaae2c4"
}
]
},
@@ -213638,17 +189283,17 @@
{
"label": "summary",
"output_name": "output1",
- "uuid": "a161c36b-e5ca-43e2-b6ec-c8e4bf530993"
+ "uuid": "1429e84c-e012-4596-a893-900b283cf0ea"
},
{
"label": "taxa",
"output_name": "output2",
- "uuid": "50d49830-a624-425e-8476-026358c44f04"
+ "uuid": "cfad7c38-abcb-4f0d-8e13-d06c73f9d6ea"
},
{
"label": "taxa_clean",
"output_name": "output3",
- "uuid": "1c833e40-98b2-42f3-a6d5-5a9d27d9ea92"
+ "uuid": "d6e34653-b42c-472c-9013-fea030efe2d5"
}
]
},
@@ -213709,17 +189354,17 @@
{
"label": "SIH_index",
"output_name": "output1",
- "uuid": "f4da174e-cd04-42d4-bbf1-38d270e13c18"
+ "uuid": "3a7776a6-c9df-4334-89a5-1882aa02ef67"
},
{
"label": "data_to_clus",
"output_name": "output2",
- "uuid": "409d3120-a20d-4922-9989-431e8ab3ea3a"
+ "uuid": "8dcb4453-0010-43cd-b7ae-d362c7d91809"
},
{
"label": "databio_table",
"output_name": "output3",
- "uuid": "d27a51e8-5d98-4958-a191-34fd938204f9"
+ "uuid": "37324d39-bdf0-47c8-b3e2-09744ecfe905"
}
]
},
@@ -213780,17 +189425,17 @@
{
"label": "SIH_plot",
"output_name": "output1",
- "uuid": "06e63c29-8df0-42f1-afe2-c694d2f68e30"
+ "uuid": "626693c4-5f50-4280-bd3c-27f339924290"
},
{
"label": "cluster_points",
"output_name": "output2",
- "uuid": "2dcc97ea-465a-4305-931c-7fee8e292adc"
+ "uuid": "0e65a0db-1607-473e-a904-e6f91ed9123c"
},
{
"label": "cluster_info",
"output_name": "output3",
- "uuid": "8f9568e8-f8fe-4059-b3f6-4d0f5bfcafdf"
+ "uuid": "3b126e94-1754-434f-95d0-80c59e64e57c"
}
]
},
@@ -213835,7 +189480,7 @@
{
"label": "eco_map",
"output_name": "output",
- "uuid": "772cd5d6-edfb-4d55-9dcc-b52354c7ce62"
+ "uuid": "5608bede-e9a3-41cb-b411-04331cc3339b"
}
]
}
@@ -214130,7 +189775,7 @@
"Understand the concept of Data Paper and learn how to produce it",
"Explain the necessity of using such tools when producing ecological metadata"
],
- "pageviews": 60,
+ "pageviews": 62,
"pub_date": "2024-01-22",
"questions": [
"How to improve the FAIR quality of an EML metadata ?",
@@ -214176,6 +189821,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -214231,10 +189880,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -214281,11 +189926,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -214330,6 +189970,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -214382,10 +190026,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -214426,10 +190066,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -214482,8 +190118,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 84,
- "visitors": 55,
+ "visit_duration": 77,
+ "visitors": 57,
"zenodo_link": "https://doi.org/10.5281/zenodo.8130567"
},
{
@@ -214660,7 +190296,6 @@
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no"
],
"feedback_mean_note": null,
@@ -214683,7 +190318,7 @@
"Visualize the data to understand them",
"Clean GBIF dataset for further analyses"
],
- "pageviews": 537,
+ "pageviews": 539,
"pub_date": "2022-10-28",
"questions": [
"How can I get ecological data from GBIF?",
@@ -214692,10 +190327,10 @@
],
"short_id": "T00129",
"short_tools": [
- "spocc_occ",
- "gdal_ogr2ogr",
"Filter1",
"Count1",
+ "gdal_ogr2ogr",
+ "spocc_occ",
"Summary_Statistics1"
],
"slides": false,
@@ -214713,11 +190348,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -214748,6 +190378,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -214803,10 +190437,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -214853,11 +190483,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -214902,6 +190527,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -214954,10 +190583,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -214998,10 +190623,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -215044,6 +190665,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -215096,10 +190721,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -215140,10 +190761,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -215186,6 +190803,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -215238,10 +190859,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -215282,10 +190899,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -215328,6 +190941,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -215380,10 +190997,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -215426,11 +191039,6 @@
"state": "exact",
"version": "3.0.0"
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- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -215474,6 +191082,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -215526,10 +191138,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -215573,11 +191181,6 @@
"state": "exact",
"version": "0.9.0"
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- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.9.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -215635,7 +191238,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 57,
- "visitors": 414,
+ "visitors": 416,
"workflows": [
{
"creators": [],
@@ -215666,7 +191269,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"Get species occurrences data\"];\n 1[\"Filter\"];\n 0 -->|output| 1;\n 2[\"Count\"];\n 0 -->|output| 2;\n 3[\"Summary Statistics\"];\n 1 -->|out_file1| 3;\n 4[\"Summary Statistics\"];\n 1 -->|out_file1| 4;\n 5[\"Filter\"];\n 1 -->|out_file1| 5;\n 6[\"Filter\"];\n 5 -->|out_file1| 6;\n 7[\"Count\"];\n 6 -->|out_file1| 7;\n 8[\"Filter\"];\n 6 -->|out_file1| 8;\n 9[\"OGR2ogr\"];\n 8 -->|out_file1| 9;\n 10[\"OGR2ogr\"];\n 8 -->|out_file1| 10;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "GBIF data Quality check and filtering workflow Feb-2020",
"outputs": [],
"parent_id": "ecology/gbif_cleaning",
@@ -215906,10 +191509,10 @@
],
"short_id": "T00127",
"short_tools": [
- "cb_eco",
+ "cb_dissim",
"cb_div",
"cb_ivr",
- "cb_dissim",
+ "cb_eco",
"cb_qecb"
],
"slides": false,
@@ -215941,6 +191544,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -215996,10 +191603,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -216046,11 +191649,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -216095,6 +191693,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216147,10 +191749,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216191,10 +191789,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -216237,6 +191831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216289,10 +191887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216333,10 +191927,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -216379,6 +191969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216431,10 +192025,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216475,10 +192065,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -216521,6 +192107,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216573,10 +192163,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216619,11 +192205,6 @@
"state": "exact",
"version": "0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -216666,6 +192247,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216718,10 +192303,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216764,11 +192345,6 @@
"state": "exact",
"version": "0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -216811,6 +192387,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -216863,10 +192443,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -216909,11 +192485,6 @@
"state": "exact",
"version": "0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -217227,7 +192798,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"IVR\"];\n 3 -->|output| 6;\n 2 -->|output| 6;\n 0 -->|output| 6;\n 1 -->|output| 6;\n 7[\"QECB\"];\n 3 -->|output| 7;\n 2 -->|output| 7;\n 4 -->|output| 7;\n 5 -->|output| 7;\n 8[\"Champs blocs indicators\"];\n 7 -->|output_rds| 8;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Champs blocs indicators",
"outputs": [
{
@@ -218018,7 +193589,7 @@
"Deal with QGIS execution management",
"Access, filter, and import GIS data using WFS webservice"
],
- "pageviews": 196,
+ "pageviews": 197,
"pub_date": "2023-10-11",
"questions": [
"How to use WFS webservice to access and import GIS data through Galaxy"
@@ -218062,6 +193633,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -218117,10 +193692,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -218167,11 +193738,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -218216,6 +193782,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -218268,10 +193838,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -218312,10 +193878,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -218371,8 +193933,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 82,
- "visitors": 168
+ "visit_duration": 81,
+ "visitors": 169
},
{
"admin_install": {
@@ -218696,6 +194258,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -218751,10 +194317,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -218801,11 +194363,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -218850,6 +194407,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -218902,10 +194463,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -218946,10 +194503,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -219112,30 +194665,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_compare\n owner: bgruening\n revisions: de72ba3ed6f2\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_bam_coverage\n owner: bgruening\n revisions: 12af64f93288\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_compute_matrix\n owner: bgruening\n revisions: 9470f29702f8\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_multi_bam_summary\n owner: bgruening\n revisions: 004aea905d4d\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_correlation\n owner: bgruening\n revisions: fd408d755394\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_fingerprint\n owner: bgruening\n revisions: 793665fff0f8\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n owner: bgruening\n revisions: ba6efa77fb79\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n owner: bgruening\n revisions: cd7e644cae1d\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n owner: devteam\n revisions: 03e9b2fbc005\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n owner: devteam\n revisions: 7def34e6cf4d\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n owner: iuc\n revisions: a1a923cd89e8\n tool_panel_section_label: BED\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n owner: iuc\n revisions: a1a923cd89e8\n tool_panel_section_label: BED\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n owner: iuc\n revisions: 640d3af5d833\n tool_panel_section_label: Peak Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.json",
- "contributions": {
- "authorship": [
- "friedue",
- "erxleben",
- "bebatut",
- "vivekbhr",
- "fidelram",
- "LeilyR",
- "pavanvidem"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "bgruening",
- "anuprulez",
- "pavanvidem",
- "gallardoalba",
- "bebatut",
- "lecorguille",
- "heylf",
- "joachimwolff",
- "LeilyR"
- ]
- },
"contributors": [
{
"id": "friedue",
@@ -219217,221 +194746,18 @@
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}
],
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+ "Read pre-processing",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Primer removal",
- "Gene regulatory network analysis",
"Sequence composition calculation",
"Enrichment analysis",
+ "Primer removal",
"Read mapping",
"Mapping",
"Sequence trimming"
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- "UseGalaxy.fr",
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],
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"Extract coverage files",
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],
- "pageviews": 6189410,
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- "samtools_idxstats",
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+ "cat1",
+ "Filter1",
"deeptools_plot_heatmap",
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+ "trim_galore",
+ "bedtools_mergebed",
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- "deeptools_bam_coverage",
- "Filter1",
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+ "fastqc",
"deeptools_bam_compare",
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+ "samtools_idxstats",
+ "deeptools_compute_matrix",
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+ "deeptools_plot_correlation",
+ "bedtools_sortbed",
+ "deeptools_bam_coverage",
+ "bowtie2",
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{
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"url": "https://usegalaxy.org",
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"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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},
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "local"
+ },
{
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{
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"state": "local"
@@ -219870,6 +195181,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "local"
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{
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"server": "https://usegalaxy.eu",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "3.0.2.0",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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{
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+ "3.3.2.0.0",
"2.5.1.1.0",
- "3.3.2.0.0"
+ "3.0.2.0"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.be/",
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"2.5.1.1.0",
- "3.0.2.0"
+ "3.0.2.0",
+ "3.3.2.0.0"
]
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{
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"state": "exact",
@@ -220497,6 +195789,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -220551,10 +195847,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.be/",
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"versions": [
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"2.5.1.1.0",
+ "2.5.7.0",
"3.3.2.0.0",
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+ "3.0.2.0"
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},
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{
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"state": "exact",
@@ -220659,6 +195946,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -220715,10 +196006,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "inexact",
"versions": [
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- "2.5.1.1.0",
"3.0.2.0",
- "2.5.7.0"
+ "2.5.7.0",
+ "2.5.1.1.0"
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{
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"state": "exact",
@@ -220823,6 +196105,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -220879,10 +196165,6 @@
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{
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@@ -220919,9 +196201,9 @@
"state": "inexact",
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+ "2.5.1.1.0",
"2.5.7.0",
- "3.0.2.0",
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+ "3.0.2.0"
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{
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"state": "exact",
@@ -220987,6 +196264,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -221043,10 +196324,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "inexact",
@@ -221100,11 +196377,6 @@
"state": "exact",
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},
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -221150,6 +196422,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -221208,10 +196484,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "missing"
@@ -221255,11 +196527,6 @@
"state": "exact",
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},
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{
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"state": "exact",
@@ -221305,6 +196572,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -221329,9 +196600,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
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+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -221343,9 +196614,9 @@
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+ "2.3.3.1",
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- "2.3.3.1",
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]
},
@@ -221369,10 +196640,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -221408,13 +196675,13 @@
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+ "2.3.4.2",
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"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
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]
},
@@ -221428,17 +196695,12 @@
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},
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{
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+ "2.4.5+galaxy1",
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@@ -221485,6 +196747,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -221542,10 +196808,6 @@
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},
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{
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@@ -221571,8 +196833,8 @@
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"0.72",
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+ "0.71",
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]
},
{
@@ -221596,12 +196858,12 @@
"0.72+galaxy1",
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"0.69",
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+ "0.65",
"0.68",
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"0.52",
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+ "0.67"
]
},
{
@@ -221611,9 +196873,9 @@
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"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -221624,11 +196886,6 @@
"state": "exact",
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},
- {
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- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -221674,6 +196931,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -221708,8 +196969,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.0",
- "2.0.3"
+ "2.0.3",
+ "2.0"
]
},
{
@@ -221732,10 +196993,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -221771,8 +197028,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0",
"2.0.3",
+ "2.0",
"2.0.1",
"2.0.2"
]
@@ -221787,11 +197044,6 @@
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},
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- "state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -221837,6 +197089,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -221894,10 +197150,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -221942,11 +197194,6 @@
"state": "exact",
"version": "2.30.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -221992,6 +197239,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -222016,8 +197267,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.27.0.0",
- "2.27.1"
+ "2.27.1",
+ "2.27.0.0"
]
},
{
@@ -222028,8 +197279,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.29.2",
- "2.30.0"
+ "2.30.0",
+ "2.29.2"
]
},
{
@@ -222052,10 +197303,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -222089,14 +197336,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.27.0.0",
"2.27.1",
- "2.29.2",
+ "2.27.0.0",
"2.30.0",
+ "2.29.2",
"2.31.1+galaxy0",
+ "2.24.0",
"2.29.0",
- "2.19.0",
- "2.24.0"
+ "2.19.0"
]
},
{
@@ -222109,17 +197356,12 @@
"state": "exact",
"version": "2.30.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.29.2",
"2.30.0",
+ "2.29.2",
"2.19.0"
]
},
@@ -222163,6 +197405,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -222216,10 +197462,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -222258,8 +197500,8 @@
"2.1.1.20160309.5",
"2.1.1.20160309.4",
"2.1.1.20160309.6",
- "2.1.1.20160309.0",
- "2.1.1.20160309.3"
+ "2.1.1.20160309.3",
+ "2.1.1.20160309.0"
]
},
{
@@ -222272,11 +197514,6 @@
"state": "exact",
"version": "2.2.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -222345,7 +197582,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 377,
- "visitors": 2247462,
+ "visitors": 2258300,
"workflows": [
{
"creators": [
@@ -222718,7 +197955,7 @@
],
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- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "GTN - ChIP Seq - Formation Of Super Structures On Xi",
"outputs": [
{
@@ -223664,7 +198901,7 @@
"Learn how to perform reproducible Infinium Human Methylation BeadChip analysis",
"Visualise differentially methylated positions using UCSC browser"
],
- "pageviews": 6181992,
+ "pageviews": 6204970,
"pub_date": "2018-08-27",
"questions": [
"Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?",
@@ -223672,12 +198909,12 @@
],
"short_id": "T00139",
"short_tools": [
- "chipeakanno_annopeaks",
- "clusterprofiler_bitr",
- "Remove beginning1",
"minfi_analysis",
+ "clusterprofiler_bitr",
"Cut1",
- "clusterprofiler_go"
+ "chipeakanno_annopeaks",
+ "clusterprofiler_go",
+ "Remove beginning1"
],
"slides": true,
"slides_recordings": false,
@@ -223723,6 +198960,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -223778,10 +199019,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -223828,11 +199065,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -223877,6 +199109,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -223929,10 +199165,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -223973,10 +199205,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -224019,6 +199247,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -224071,10 +199303,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -224115,10 +199343,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -224161,6 +199385,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -224213,10 +199441,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -224259,10 +199483,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -224306,6 +199526,10 @@
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@@ -224451,6 +199667,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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@@ -224549,10 +199765,6 @@
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@@ -224596,6 +199808,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "missing"
+ },
{
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@@ -224648,10 +199864,6 @@
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@@ -224694,10 +199906,6 @@
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@@ -224751,7 +199959,7 @@
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@@ -225083,7 +200291,7 @@
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Infinium Human Methylation BeadChip",
"outputs": [
{
@@ -225651,28 +200859,6 @@
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@@ -225914,15 +200919,15 @@
],
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+ "Gene regulatory network analysis",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
- "Gene regulatory network analysis",
"Sequence composition calculation",
"Enrichment analysis",
+ "Generation",
"Read mapping",
"Mapping",
- "Generation",
+ "Sequence alignment",
"Genome indexing"
],
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@@ -225967,7 +200971,7 @@
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"pub_date": "2016-12-20",
"questions": [
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],
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+ "deeptools_plot_heatmap",
+ "bedtools_intersectbed",
"deeptools_correct_gc_bias",
- "deeptools_multi_bam_summary",
- "samtools_idxstats",
+ "macs2_callpeak",
"fastqc",
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+ "trimmomatic",
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+ "samtools_idxstats",
+ "deeptools_multi_bam_summary",
"deeptools_compute_matrix",
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"deeptools_compute_gc_bias",
- "bwa",
"deeptools_plot_correlation",
- "trimmomatic",
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- "bedtools_intersectbed"
+ "deeptools_plot_fingerprint"
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{
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"url": "https://usegalaxy.org",
@@ -226078,6 +201077,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -226133,10 +201136,6 @@
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"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -226183,11 +201182,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -226232,6 +201226,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"state": "missing"
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{
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+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
"outputs": [
{
@@ -228871,7 +203795,7 @@
{
"label": "output_overlapping_peaks",
"output_name": "output",
- "uuid": "7a601b31-0d9e-410e-9eda-67196a74357b"
+ "uuid": "a52c1a9e-b404-4c4e-90ff-60d6760bb802"
}
]
},
@@ -228919,7 +203843,7 @@
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"label": "output_g1e_peaks",
"output_name": "output",
- "uuid": "c8f9f7f3-2dbf-46d2-b40c-f15e5506bfd2"
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}
]
},
@@ -228967,7 +203891,7 @@
{
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"output_name": "output",
- "uuid": "eb556dad-3fd6-4119-b413-894178ecad10"
+ "uuid": "6526a0f0-21c1-4ae2-a20f-2db39b92687a"
}
]
}
@@ -229116,23 +204040,6 @@
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@@ -229173,209 +204080,25 @@
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- ],
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],
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- "Data handling",
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+ "Visualisation",
+ "Gene regulatory network analysis",
+ "Sequence trimming",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Formatting",
- "Sequence alignment analysis",
- "Primer removal",
- "Gene regulatory network analysis",
"Sequence composition calculation",
+ "Formatting",
+ "Data handling",
"Enrichment analysis",
+ "Primer removal",
+ "Sequence alignment analysis",
"Read mapping",
"Mapping",
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+ "Read pre-processing"
],
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"exact_supported_servers": [],
@@ -229403,7 +204126,7 @@
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],
- "pageviews": 6282592,
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"macs2_callpeak",
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+ "deeptools_compute_matrix",
+ "picard_MarkDuplicates",
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+ "bowtie2"
],
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@@ -229491,6 +204214,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -229546,10 +204273,6 @@
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},
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -229596,11 +204319,6 @@
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"usegalaxy": true
},
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -229646,287 +204364,7 @@
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- "state": "missing"
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- "state": "local"
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- "state": "local"
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{
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- "state": "missing"
+ "state": "local"
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{
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+ "server": "https://usegalaxy.org",
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@@ -230151,7 +204709,7 @@
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@@ -230159,59 +204717,45 @@
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@@ -230233,6 +204777,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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- "3.1.2.0.1"
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+ "state": "inexact",
+ "versions": [
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+ ]
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{
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{
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- "3.5.2+galaxy0"
+ "3.5.2+galaxy0",
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{
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{
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@@ -230393,6 +204934,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -230415,8 +204960,11 @@
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+ "state": "inexact",
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+ "3.5.1.0.1"
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{
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{
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{
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- "version": "1.1.1"
+ "state": "inexact",
+ "versions": [
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+ "3.5.2+galaxy0"
+ ]
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{
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{
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{
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+ "version": "3.3.2.0.1"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
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@@ -230547,6 +205089,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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+ "state": "exact",
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{
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+ "version": "1.1.1"
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "9.3+galaxy1"
+ ]
},
{
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{
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+ "2.5.2+galaxy2"
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@@ -231199,6 +205870,10 @@
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{
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{
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+ "2.31.1+galaxy0",
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@@ -231528,6 +206183,10 @@
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{
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@@ -231844,6 +206489,10 @@
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},
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{
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@@ -231992,6 +206632,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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@@ -232047,10 +206691,6 @@
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{
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@@ -232096,11 +206736,6 @@
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{
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"state": "exact",
@@ -232146,6 +206781,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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{
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@@ -232185,8 +206824,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -232209,10 +206848,6 @@
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{
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"state": "inexact",
@@ -232270,47 +206905,22 @@
"4.7+galaxy0",
"4.4+galaxy0",
"1.16.3",
- "1.6",
"1.16.1",
- "3.5+galaxy0",
+ "1.6",
+ "4.0+galaxy1",
"3.4+galaxy2",
- "4.6+galaxy0",
- "1.16",
+ "1.1.a",
+ "3.7+galaxy0",
+ "3.5+galaxy2",
"3.4+galaxy1",
"4.6+galaxy1",
"3.4+galaxy0",
- "3.7+galaxy0",
- "1.1.a",
- "4.8+galaxy0",
+ "1.16",
"4.9+galaxy0",
- "4.0+galaxy1",
"3.5+galaxy1",
- "3.5+galaxy2"
- ]
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- {
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- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
"3.5+galaxy0",
- "3.4+galaxy2",
"4.6+galaxy0",
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- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
+ "4.8+galaxy0"
]
},
{
@@ -232358,6 +206968,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -232410,10 +207024,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -232454,10 +207064,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -232522,7 +207128,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 263,
- "visitors": 2297498,
+ "visitors": 2308533,
"workflows": [
{
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@@ -232808,7 +207414,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "ATAC-seq GTM",
"outputs": [
{
@@ -234519,18 +209125,18 @@
"dir": "topics/epigenetics/tutorials/cut_and_run",
"draft": true,
"edam_operation": [
- "Visualisation",
- "Data handling",
"Peak calling",
+ "Visualisation",
+ "Gene regulatory network analysis",
+ "Read pre-processing",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Formatting",
- "Sequence alignment analysis",
- "Primer removal",
- "Gene regulatory network analysis",
"Sequence composition calculation",
+ "Data handling",
+ "Formatting",
"Enrichment analysis",
+ "Primer removal",
+ "Sequence alignment analysis",
"Read mapping",
"Mapping",
"Sequence trimming"
@@ -234541,7 +209147,9 @@
"feedback_number": 0,
"hands_on": true,
"id": "epigenetics/cut_and_run",
- "inexact_supported_servers": [],
+ "inexact_supported_servers": [
+ "UseGalaxy.cz"
+ ],
"js_requirements": {
"mathjax": null,
"mermaid": false
@@ -234554,13 +209162,13 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-03-06",
+ "mod_date": "2024-12-11",
"objectives": [
"Apply appropriate analysis and quality control steps for CUT&RUN",
"Apply an enrichment analysis and a robust peak detection",
"Find protein binding motifs"
],
- "pageviews": 2772,
+ "pageviews": 2837,
"pub_date": "2024-03-06",
"questions": [
"Which binding motif has the transcription factor GATA1?",
@@ -234569,33 +209177,38 @@
],
"short_id": "T00424",
"short_tools": [
- "bowtie2",
- "meme_chip",
- "trim_galore",
- "pygenomeTracks",
- "picard_MarkDuplicates",
- "deeptools_plot_heatmap",
- "deeptools_compute_matrix",
"Filter1",
"pe_histogram",
"Grep1",
+ "__EXTRACT_DATASET__",
+ "deeptools_compute_matrix",
+ "Extract genomic DNA 1",
+ "idr",
+ "deeptools_plot_heatmap",
+ "macs2_callpeak",
+ "cutadapt",
"bamFilter",
"__FLATTEN__",
"wig_to_bigWig",
- "bedtools_bamtobed",
- "idr",
"fastqc",
- "cutadapt",
- "macs2_callpeak",
- "__EXTRACT_DATASET__",
+ "bedtools_bamtobed",
+ "bowtie2",
"bedtools_intersectbed",
- "Extract genomic DNA 1"
+ "meme_chip",
+ "pygenomeTracks",
+ "picard_MarkDuplicates"
],
"slides": false,
"slides_recordings": false,
"supported_servers": {
"exact": [],
- "inexact": []
+ "inexact": [
+ {
+ "name": "UseGalaxy.cz",
+ "url": "https://usegalaxy.cz/",
+ "usegalaxy": false
+ }
+ ]
},
"supported_servers_matrix": {
"servers": [
@@ -234619,6 +209232,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -234674,10 +209291,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -234724,11 +209337,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -234750,148 +209358,6 @@
}
],
"tools": [
- {
- "id": " https://toolshed.g2.bx.psu.edu/view/bgruening/trim_galore/cd7e644cae1d",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
- },
- {
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "trim_galore/cd7e644cae1d"
- },
{
"id": "Filter1",
"servers": [
@@ -234915,6 +209381,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -234967,10 +209437,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -235011,10 +209477,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -235057,6 +209519,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -235109,10 +209575,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -235153,10 +209615,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -235199,6 +209657,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -235251,10 +209713,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -235295,10 +209753,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -235341,6 +209795,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -235393,10 +209851,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -235437,10 +209891,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -235483,6 +209933,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -235542,10 +209996,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -235595,11 +210045,6 @@
"state": "exact",
"version": "3.3.2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.2.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -235645,6 +210090,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -235669,8 +210118,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.5.1.0.1",
- "3.1.2.0.1"
+ "3.1.2.0.1",
+ "3.5.1.0.1"
]
},
{
@@ -235702,10 +210151,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -235755,11 +210200,6 @@
"state": "exact",
"version": "3.3.2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.2.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -235805,6 +210245,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -235861,10 +210305,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -235910,11 +210350,6 @@
"state": "exact",
"version": "2.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -235960,6 +210395,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236016,10 +210455,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -236068,11 +210503,6 @@
"state": "exact",
"version": "2.5.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236118,6 +210548,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236172,10 +210606,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -236217,12 +210647,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -236231,11 +210661,6 @@
"state": "exact",
"version": "2.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236281,6 +210706,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236315,9 +210744,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -236341,10 +210770,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -236380,13 +210805,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -236395,12 +210820,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -236409,11 +210834,6 @@
"state": "exact",
"version": "2.4.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.5+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236459,6 +210879,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236516,10 +210940,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -236570,9 +210990,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -236583,11 +211003,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236633,6 +211048,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236690,10 +211109,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -236719,8 +211134,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -236744,12 +211159,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -236759,9 +211174,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -236772,11 +211187,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236822,6 +211232,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -236879,10 +211293,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -236932,11 +211342,6 @@
"state": "exact",
"version": "2.18.2.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -236982,6 +211387,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237039,10 +211448,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -237092,11 +211497,6 @@
"state": "exact",
"version": "2.18.2.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -237144,6 +211544,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237204,16 +211608,12 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "2.30.0+galaxy2",
- "2.31.1+galaxy0"
+ "2.31.1+galaxy0",
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]
},
{
@@ -237255,17 +211655,6 @@
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- "2.30.0+galaxy2",
- "2.31.1+galaxy0",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -237311,6 +211700,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237371,10 +211764,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -237412,10 +211801,10 @@
"2.27.0.0",
"2.29.2",
"2.31.1+galaxy0",
+ "2.29.0",
"2.24.0",
"2.19.0",
- "2.30.0",
- "2.29.0"
+ "2.30.0"
]
},
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@@ -237428,11 +211817,6 @@
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},
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- "state": "exact",
- "version": "2.30.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -237478,6 +211862,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237535,10 +211923,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -237586,11 +211970,6 @@
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- "version": "2.30.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -237636,6 +212015,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237696,10 +212079,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -237738,10 +212117,10 @@
"2.29.2",
"2.30.0",
"2.31.1+galaxy0",
- "2.27.1+galaxy1",
"2.19.0",
"2.29.0",
- "2.24.0"
+ "2.24.0",
+ "2.27.1+galaxy1"
]
},
{
@@ -237754,11 +212133,6 @@
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- "state": "exact",
- "version": "2.30.0+galaxy1"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -237808,6 +212182,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -237861,10 +212239,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -237909,10 +212283,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
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"state": "exact",
@@ -237957,6 +212327,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238009,10 +212383,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -238057,10 +212427,6 @@
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -238105,6 +212471,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238161,10 +212531,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -238213,11 +212579,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "2.1.1.20160309.6"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -238263,6 +212624,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238316,10 +212681,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -238358,8 +212719,8 @@
"2.1.1.20160309.5",
"2.1.1.20160309.4",
"2.1.1.20160309.6",
- "2.1.1.20160309.0",
- "2.1.1.20160309.3"
+ "2.1.1.20160309.3",
+ "2.1.1.20160309.0"
]
},
{
@@ -238372,11 +212733,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -238422,6 +212778,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238475,10 +212835,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -238522,10 +212878,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -238570,6 +212922,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238622,10 +212978,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -238669,11 +213021,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -238718,6 +213065,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238773,10 +213124,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -238822,11 +213169,6 @@
"state": "exact",
"version": "3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -238872,6 +213214,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -238911,8 +213257,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -238935,10 +213281,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -238996,47 +213338,22 @@
"4.7+galaxy0",
"4.4+galaxy0",
"1.16.3",
- "1.6",
"1.16.1",
- "3.5+galaxy0",
+ "1.6",
+ "4.0+galaxy1",
"3.4+galaxy2",
- "4.6+galaxy0",
- "1.16",
+ "1.1.a",
+ "3.7+galaxy0",
+ "3.5+galaxy2",
"3.4+galaxy1",
"4.6+galaxy1",
"3.4+galaxy0",
- "3.7+galaxy0",
- "1.1.a",
- "4.8+galaxy0",
+ "1.16",
"4.9+galaxy0",
- "4.0+galaxy1",
"3.5+galaxy1",
- "3.5+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "4.8+galaxy1",
- "4.9+galaxy1",
- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
"3.5+galaxy0",
- "3.4+galaxy2",
"4.6+galaxy0",
- "3.4+galaxy1",
- "4.6+galaxy1",
- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
+ "4.8+galaxy0"
]
},
{
@@ -239084,6 +213401,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -239136,10 +213457,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -239180,10 +213497,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -239212,7 +213525,6 @@
"time_estimation": "3h",
"title": "CUT&RUN data analysis",
"tools": [
- " https://toolshed.g2.bx.psu.edu/view/bgruening/trim_galore/cd7e644cae1d",
"Filter1",
"Grep1",
"__EXTRACT_DATASET__",
@@ -239256,12 +213568,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json"
},
- "version": 1,
+ "version": 2,
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 83,
- "visitors": 2160,
+ "visit_duration": 85,
+ "visitors": 2215,
"workflows": [
{
"creators": [],
@@ -239414,7 +213726,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nbed file with genes\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nctcf peaks\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Filter\"];\n 1 -->|output| 4;\n 5[\"FastQC\"];\n 2 -->|output| 5;\n 6[\"ATAC remove nextera adapters with cutadapt\"];\n 3 -->|output| 6;\n 2 -->|output| 6;\n 7[\"FastQC\"];\n 3 -->|output| 7;\n 8[\"bedtools Intersect intervals\"];\n 4 -->|out_file1| 8;\n 0 -->|output| 8;\n 9[\"FastQC\"];\n 6 -->|out2| 9;\n 10[\"Bowtie2\"];\n 6 -->|out1| 10;\n 6 -->|out2| 10;\n 11[\"FastQC\"];\n 6 -->|out1| 11;\n 12[\"Filter BAM ATAC\"];\n 10 -->|output| 12;\n 13[\"MarkDuplicates\"];\n 12 -->|out_file1| 13;\n 14[\"bedtools BAM to BED\"];\n 13 -->|outFile| 14;\n 15[\"Paired-end histogram\"];\n 13 -->|outFile| 15;\n 16[\"MACS2 callpeak\"];\n 14 -->|output| 16;\n 17[\"Wig/BedGraph-to-bigWig\"];\n 16 -->|output_treat_pileup| 17;\n 18[\"computeMatrix\"];\n 17 -->|out_file1| 18;\n 0 -->|output| 18;\n 19[\"pyGenomeTracks\"];\n 17 -->|out_file1| 19;\n 16 -->|output_narrowpeaks| 19;\n 0 -->|output| 19;\n 1 -->|output| 19;\n 20[\"computeMatrix\"];\n 17 -->|out_file1| 20;\n 8 -->|output| 20;\n 65159c9c-050b-4069-8704-8f66c0563a98[\"Output\\ncomputeMatrix on input dataset(s): Matrix\"];\n 20 --> 65159c9c-050b-4069-8704-8f66c0563a98;\n style 65159c9c-050b-4069-8704-8f66c0563a98 stroke:#2c3143,stroke-width:4px;\n 21[\"plotHeatmap\"];\n 18 -->|outFileName| 21;\n 22[\"plotHeatmap\"];\n 20 -->|outFileName| 22;\n 74a36643-b88f-4378-8f9c-c1b20ee2651e[\"Output\\nplotHeatmap on input dataset(s): Image\"];\n 22 --> 74a36643-b88f-4378-8f9c-c1b20ee2651e;\n style 74a36643-b88f-4378-8f9c-c1b20ee2651e stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "ATAC-seq GTM",
"outputs": [
{
@@ -240856,25 +215168,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.json",
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- "authorship": [
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- "erxleben",
- "bebatut",
- "vivekbhr",
- "fidelram"
- ],
- "reviewing": [
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- "hexylena",
- "nsoranzo",
- "fidelram",
- "bgruening",
- "njall",
- "bebatut",
- "mblue9"
- ]
- },
"contributors": [
{
"id": "friedue",
@@ -240937,178 +215230,19 @@
"name": "Fidel Ramirez",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/fidelram/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/fidelram.json"
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- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
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- "elixir_node": "uk",
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- "id": "nsoranzo",
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- "linkedin": "nicola-soranzo-7884125",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "fediverse_flavor": "mastodon",
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- "linkedin": "bgruening",
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
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- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
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- },
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- "contact_for_training": true,
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- "location": {
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- "lat": 45.77,
- "lon": 3.08
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- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "name": "Maria Doyle",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification",
"draft": true,
"edam_operation": [
"Peak calling",
+ "Gene regulatory network analysis",
+ "Read pre-processing",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Primer removal",
- "Gene regulatory network analysis",
"Sequence composition calculation",
"Enrichment analysis",
+ "Primer removal",
"Read mapping",
"Sequence trimming"
],
@@ -241123,7 +215257,6 @@
"inexact_supported_servers": [
"Galaxy@AuBi",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -241147,7 +215280,7 @@
"Extract coverage files",
"Call enriched regions or peaks"
],
- "pageviews": 2508,
+ "pageviews": 2518,
"pub_date": "2017-09-18",
"questions": [
"How is raw ChIP-seq data processed and analyzed?",
@@ -241160,20 +215293,20 @@
],
"short_id": "T00138",
"short_tools": [
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- "samtools_idxstats",
- "fastqc",
"deeptools_plot_heatmap",
- "deeptools_compute_matrix",
- "deeptools_plot_fingerprint",
- "bowtie2",
- "deeptools_compute_gc_bias",
+ "trim_galore",
"macs2_callpeak",
- "deeptools_bam_coverage",
+ "fastqc",
+ "deeptools_bam_compare",
+ "samtools_idxstats",
"bam_to_sam",
+ "deeptools_multi_bam_summary",
+ "deeptools_compute_matrix",
+ "deeptools_compute_gc_bias",
"deeptools_plot_correlation",
- "deeptools_bam_compare",
- "trim_galore"
+ "deeptools_bam_coverage",
+ "bowtie2",
+ "deeptools_plot_fingerprint"
],
"slides": false,
"slides_recordings": false,
@@ -241196,11 +215329,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -241240,6 +215368,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -241295,10 +215427,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -241345,11 +215473,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -241394,6 +215517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -241449,10 +215576,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -241502,17 +215625,6 @@
"state": "exact",
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},
- {
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- "state": "inexact",
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- "3.3.2.0.0",
- "3.5.2+galaxy0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -241530,8 +215642,8 @@
"3.3.2.0.0",
"3.5.2+galaxy0",
"2.5.0.0",
- "3.3.0.0.0",
"2.3.5.0",
+ "3.3.0.0.0",
"3.1.2.0.0"
]
},
@@ -241570,6 +215682,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -241594,9 +215710,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
+ "3.3.0.0.0",
"3.5.1.0.0",
- "3.3.0.0.0"
+ "3.1.2.0.0"
]
},
{
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"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
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{
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@@ -241683,17 +215795,6 @@
"state": "exact",
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},
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- "3.5.2+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -241706,17 +215807,17 @@
"server": "https://usegalaxy.org",
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"versions": [
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- "3.5.1.0.0",
"3.3.0.0.0",
+ "3.5.1.0.0",
+ "3.1.2.0.0",
"3.5.4+galaxy0",
- "3.0.2.0",
"3.3.2.0.0",
+ "3.0.2.0",
"3.5.2+galaxy0",
"2.5.0.0",
- "3.2.0.0.0",
"2.3.5.0",
- "3.2.1.0.0"
+ "3.2.1.0.0",
+ "3.2.0.0.0"
]
},
{
@@ -241754,6 +215855,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -241809,10 +215914,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -241862,17 +215963,6 @@
"state": "exact",
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},
- {
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- "state": "inexact",
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- "3.5.4+galaxy0",
- "3.3.2.0.0",
- "3.5.2+galaxy0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -241890,9 +215980,9 @@
"3.3.2.0.0",
"3.5.2+galaxy0",
"2.5.0.0",
- "3.3.0.0.0",
"3.1.2.0.0",
- "2.3.5.0"
+ "2.3.5.0",
+ "3.3.0.0.0"
]
},
{
@@ -241930,6 +216020,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -241989,10 +216083,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -242042,17 +216132,6 @@
"state": "exact",
"version": "2.5.1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.5.2+galaxy0",
- "3.5.4+galaxy0",
- "3.3.2.0.0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242101,6 +216180,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -242125,8 +216208,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
- "3.5.1.0.0"
+ "3.5.1.0.0",
+ "3.1.2.0.0"
]
},
{
@@ -242160,10 +216243,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -242213,17 +216292,6 @@
"state": "exact",
"version": "2.5.1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.5.4+galaxy0",
- "3.3.2.0.0",
- "3.5.2+galaxy0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242236,14 +216304,14 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
"3.5.1.0.0",
+ "3.1.2.0.0",
"3.5.4+galaxy0",
"3.3.2.0.0",
"3.5.2+galaxy0",
"2.5.0.0",
- "3.3.0.0.0",
- "2.3.5.0"
+ "2.3.5.0",
+ "3.3.0.0.0"
]
},
{
@@ -242281,6 +216349,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -242305,8 +216377,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
- "3.5.1.0.0"
+ "3.5.1.0.0",
+ "3.1.2.0.0"
]
},
{
@@ -242340,10 +216412,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -242393,17 +216461,6 @@
"state": "exact",
"version": "2.5.1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.3.2.0.0",
- "3.5.4+galaxy0",
- "3.5.2+galaxy0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242416,8 +216473,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
"3.5.1.0.0",
+ "3.1.2.0.0",
"3.3.2.0.0",
"3.5.4+galaxy0",
"3.5.2+galaxy0",
@@ -242461,6 +216518,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -242520,10 +216581,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -242573,17 +216630,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.3.2.0.0",
- "3.5.4+galaxy0",
- "3.5.2+galaxy0",
- "3.3.0.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242641,6 +216687,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -242665,8 +216715,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.5.1.0.1",
- "3.1.2.0.1"
+ "3.1.2.0.1",
+ "3.5.1.0.1"
]
},
{
@@ -242700,10 +216750,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -242753,17 +216799,6 @@
"state": "exact",
"version": "2.5.1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.3.2.0.1",
- "3.5.4+galaxy0",
- "3.5.2+galaxy0",
- "3.3.0.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242776,8 +216811,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "3.5.1.0.1",
"3.1.2.0.1",
+ "3.5.1.0.1",
"3.3.2.0.1",
"3.5.4+galaxy0",
"3.0.2.0",
@@ -242822,6 +216857,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -242880,10 +216919,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -242927,14 +216962,6 @@
"state": "exact",
"version": "0.4.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.6.3",
- "0.6.7+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -242995,6 +217022,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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@@ -243050,10 +217081,6 @@
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- "state": "missing"
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"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -243099,11 +217126,6 @@
"server": "https://usegalaxy.eu",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -243152,6 +217174,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -243176,9 +217202,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -243190,9 +217216,9 @@
"state": "inexact",
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+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -243216,10 +217242,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -243266,27 +217288,12 @@
"state": "exact",
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},
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- "2.3.4.3",
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- "2.5.3+galaxy1",
- "2.5.0+galaxy0",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
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"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -243302,9 +217309,9 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
"2.4.5+galaxy1",
- "2.4.2+galaxy0",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
@@ -243345,6 +217352,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -243370,8 +217381,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -243406,10 +217417,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -243435,8 +217442,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -243468,17 +217475,6 @@
"state": "exact",
"version": "0.69"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "0.73+galaxy0",
- "0.72",
- "0.74+galaxy0",
- "0.74+galaxy1"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -243527,6 +217523,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -243566,8 +217566,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.0",
- "2.0.3"
+ "2.0.3",
+ "2.0"
]
},
{
@@ -243590,10 +217590,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -243642,15 +217638,6 @@
"state": "exact",
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{
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"state": "inexact",
@@ -243699,6 +217686,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -243755,10 +217746,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -243807,15 +217794,6 @@
"state": "exact",
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},
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- "state": "inexact",
- "versions": [
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- "2.2.9.1+galaxy0",
- "2.1.1.20160309.6"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -243885,8 +217863,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 170,
- "visitors": 1647,
+ "visit_duration": 171,
+ "visitors": 1654,
"workflows": [
{
"creators": [],
@@ -244166,7 +218144,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"IdxStats\"];\n 0 -->|output| 9;\n 10[\"bamCoverage\"];\n 0 -->|output| 10;\n 11[\"bamCoverage\"];\n 0 -->|output| 11;\n 12[\"plotFingerprint\"];\n 4 -->|output| 12;\n 0 -->|output| 12;\n 13[\"computeGCBias\"];\n 4 -->|output| 13;\n 14[\"IdxStats\"];\n 4 -->|output| 14;\n 15[\"bamCoverage\"];\n 4 -->|output| 15;\n 16[\"bamCoverage\"];\n 4 -->|output| 16;\n 17[\"bamCompare\"];\n 0 -->|output| 17;\n 4 -->|output| 17;\n 18[\"bamCompare\"];\n 0 -->|output| 18;\n 4 -->|output| 18;\n 19[\"MACS2 callpeak\"];\n 4 -->|output| 19;\n 0 -->|output| 19;\n 20[\"multiBamSummary\"];\n 7 -->|output| 20;\n 6 -->|output| 20;\n 5 -->|output| 20;\n 4 -->|output| 20;\n 3 -->|output| 20;\n 2 -->|output| 20;\n 1 -->|output| 20;\n 0 -->|output| 20;\n 21[\"computeMatrix\"];\n 18 -->|outFileName| 21;\n 8 -->|output| 21;\n 22[\"computeMatrix\"];\n 18 -->|outFileName| 22;\n 8 -->|output| 22;\n 23[\"plotCorrelation\"];\n 20 -->|outFile| 23;\n 24[\"plotHeatmap\"];\n 21 -->|outFileName| 24;\n 25[\"plotHeatmap\"];\n 22 -->|outFileName| 25;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Identification Of The Binding Sites Of The Estrogen Receptor - Chip Seq",
"outputs": [],
"parent_id": "epigenetics/estrogen-receptor-binding-site-identification",
@@ -244270,7 +218248,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n 2[\"Trim Galore!\"];\n 0 -->|output| 2;\n 3[\"Bowtie2\"];\n 2 -->|trimmed_reads_single| 3;\n 4[\"BAM-to-SAM\"];\n 3 -->|output| 4;",
- "modified": "2024-12-09 08:53:33 +0000",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Identification Of The Binding Sites Of The Estrogen Receptor - Qc Mapping",
"outputs": [],
"parent_id": "epigenetics/estrogen-receptor-binding-site-identification",
@@ -244374,22 +218352,6 @@
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- "willdurand",
- "bgruening",
- "njall"
- ]
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"contributors": [
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@@ -244410,168 +218372,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/dpryan79/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/dpryan79.json"
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- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
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- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
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}
],
"dir": "topics/epigenetics/tutorials/methylation-seq",
@@ -244579,9 +218379,9 @@
"topic_3173"
],
"edam_operation": [
+ "Sequencing quality control",
"Sequence composition calculation",
- "Statistical calculation",
- "Sequencing quality control"
+ "Statistical calculation"
],
"edam_topic": [
"Epigenomics"
@@ -244616,7 +218416,7 @@
"Learn how to analyse methylation data",
"Get a first intuition what are common pitfalls."
],
- "pageviews": 20783,
+ "pageviews": 20935,
"pub_date": "2017-02-16",
"questions": [
"What is methylation and why it cannot be recognised by a normal NGS procedure?",
@@ -244625,15 +218425,15 @@
],
"short_id": "T00142",
"short_tools": [
+ "tp_tail_tool",
+ "deeptools_plot_profile",
"fastqc",
+ "replace_column_with_key_value_file",
"tp_awk_tool",
- "deeptools_compute_matrix",
- "deeptools_plot_profile",
"bwameth",
- "replace_column_with_key_value_file",
- "tp_tail_tool",
- "metilene",
- "pileometh"
+ "pileometh",
+ "deeptools_compute_matrix",
+ "metilene"
],
"slides": false,
"slides_recordings": false,
@@ -244695,6 +218495,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -244750,10 +218554,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -244800,11 +218600,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -244849,6 +218644,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -244908,10 +218707,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -244961,17 +218756,6 @@
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},
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -245020,6 +218804,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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@@ -245191,6 +218964,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -245284,8 +219057,8 @@
"server": "https://usegalaxy.cz/",
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{
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
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{
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+ "state": "missing"
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{
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@@ -245545,7 +219153,7 @@
"server": "https://galaxytrakr.org/",
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"server": "http://galaxy.interactomix.com/",
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{
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+ "0.2"
]
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{
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{
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{
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+ "state": "inexact",
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{
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- "1.1.1",
- "9.3+galaxy1",
- "9.3+galaxy0"
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+ "version": "0.1"
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{
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{
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+ "version": "0.1"
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{
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{
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@@ -245678,6 +219271,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -245700,8 +219297,11 @@
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{
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+ "state": "inexact",
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+ "1.1.1"
+ ]
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{
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+ "state": "inexact",
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{
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{
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@@ -245799,8 +219392,13 @@
},
{
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+ "state": "inexact",
+ "versions": [
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+ "1.1.1",
+ "9.3+galaxy1",
+ "9.3+galaxy0"
+ ]
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{
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
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@@ -245832,6 +219430,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -245854,28 +219456,17 @@
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{
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- "0.73+galaxy0",
- "0.72"
- ]
+ "state": "exact",
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{
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+ "state": "missing"
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{
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- "0.69"
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{
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{
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+ "9.3+galaxy1"
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{
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- "0.71"
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+ "state": "missing"
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{
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- "versions": [
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+ "state": "missing"
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{
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- "versions": [
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+ "state": "missing"
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{
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"state": "exact",
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+ "version": "1.1.0"
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{
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{
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- "0.73+galaxy0",
- "0.72",
- "0.74+galaxy0",
- "0.74+galaxy1"
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+ "version": "1.1.0"
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{
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- "versions": [
- "0.72+galaxy1",
- "0.73+galaxy0"
- ]
+ "state": "exact",
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{
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"state": "exact",
- "version": "0.68"
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{
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- "0.74+galaxy0",
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- "0.71",
- "0.74+galaxy1",
- "0.70"
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+ "state": "exact",
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{
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"state": "missing"
}
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+ "version": "1.1.0"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68",
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@@ -246027,6 +219579,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -246049,15 +219605,28 @@
},
{
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- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.72+galaxy1",
+ "0.72",
+ "0.73+galaxy0"
+ ]
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.72+galaxy1",
+ "0.73+galaxy0",
+ "0.69"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -246079,13 +219648,12 @@
"server": "http://galaxy.interactomix.com/",
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
},
{
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@@ -246101,61 +219669,68 @@
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{
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- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.72+galaxy1",
+ "0.72",
+ "0.71",
+ "0.65"
+ ]
},
{
"server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
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- {
- "server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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- "0.2.0.4"
+ "0.74+galaxy0"
]
},
{
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+ "server": "https://usegalaxy.be/",
"state": "exact",
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+ "version": "0.68"
},
{
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+ "server": "https://usegalaxy.cz/",
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- "version": "0.2.0.3"
+ "version": "0.68"
},
{
- "server": "https://usegalaxy.fr/",
- "state": "missing"
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.68"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
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- "0.2.2+galaxy1",
- "0.2.3+galaxy0"
+ "0.72+galaxy1",
+ "0.73+galaxy0"
]
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{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "0.2.0.3"
+ "version": "0.68"
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{
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- "0.2.2+galaxy1",
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- "0.2.7+galaxy0",
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+ "0.72+galaxy1",
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+ "0.73+galaxy0",
+ "0.74+galaxy0",
+ "0.69",
+ "0.71",
+ "0.74+galaxy1",
+ "0.70"
]
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+ "version": "0.68"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3",
"servers": [
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@@ -246188,6 +219763,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -246210,8 +219789,7 @@
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{
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+ "state": "missing"
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{
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@@ -246241,10 +219819,6 @@
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{
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"state": "missing"
@@ -246275,21 +219849,174 @@
},
{
"server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.2.0.4",
+ "0.2.2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "0.2.0.3"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.2.0.3"
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+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "0.2.2",
+ "0.2.2+galaxy1",
+ "0.2.3+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.2.0.3"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "inexact",
+ "versions": [
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+ "0.2.2+galaxy1",
+ "0.2.6+galaxy0",
+ "0.2.7+galaxy0",
+ "0.2.3+galaxy0"
+ ]
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ "server": "http://igg.cloud.ba.infn.it/galaxy",
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+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
"state": "exact",
"version": "0.2.6.1"
},
{
- "server": "https://usegalaxy.cz/",
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
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+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
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+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
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+ "state": "missing"
+ },
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+ "server": "https://neo.engr.uconn.edu/",
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+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
"state": "exact",
"version": "0.2.6.1"
},
{
- "server": "https://usegalaxy.eu",
+ "server": "https://usegalaxy.cz/",
"state": "exact",
"version": "0.2.6.1"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.2.6.1"
},
@@ -246350,8 +220077,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 126,
- "visitors": 11852,
+ "visit_duration": 127,
+ "visitors": 11948,
"workflows": [
{
"creators": [],
@@ -246362,7 +220089,7 @@
"report": null,
"subworkflows": false
},
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+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n 9[label=\"FastQC\"]\n 0 -> 9 [label=\"output\"]\n 10[label=\"FastQC\"]\n 1 -> 10 [label=\"output\"]\n 11[label=\"bwameth\"]\n 0 -> 11 [label=\"output\"]\n 1 -> 11 [label=\"output\"]\n 12[label=\"Replace column\"]\n 3 -> 12 [label=\"output\"]\n 4 -> 12 [label=\"output\"]\n 13[label=\"metilene\"]\n 2 -> 13 [label=\"output\"]\n 5 -> 13 [label=\"output\"]\n 3 -> 13 [label=\"output\"]\n 8 -> 13 [label=\"output\"]\n 7 -> 13 [label=\"output\"]\n 6 -> 13 [label=\"output\"]\n 14[label=\"MethylDackel\"]\n 11 -> 14 [label=\"output\"]\n 15[label=\"MethylDackel\"]\n 11 -> 15 [label=\"output\"]\n 16[label=\"Select last\"]\n 12 -> 16 [label=\"outfile_replace\"]\n 17[label=\"Select last\"]\n 15 -> 17 [label=\"outFileExtractCpGFraction\"]\n 18[label=\"computeMatrix\"]\n 16 -> 18 [label=\"outfile\"]\n 2 -> 18 [label=\"output\"]\n 19[label=\"Text reformatting\"]\n 17 -> 19 [label=\"outfile\"]\n 20[label=\"computeMatrix\"]\n 19 -> 20 [label=\"outfile\"]\n 2 -> 20 [label=\"output\"]\n 21[label=\"plotProfile\"]\n 20 -> 21 [label=\"outFileName\"]\n kc5b35deaecfd4bc287db780aaa72e039[color=lightseagreen,label=\"Output\\nplot_profile_tabular\"]\n 21 -> kc5b35deaecfd4bc287db780aaa72e039\n}",
"history": [
{
"hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
@@ -246630,8 +220357,8 @@
}
],
"license": null,
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 0 -->|output| 9;\n 10[\"FastQC\"];\n 1 -->|output| 10;\n 11[\"bwameth\"];\n 0 -->|output| 11;\n 1 -->|output| 11;\n 12[\"Replace column\"];\n 3 -->|output| 12;\n 4 -->|output| 12;\n 13[\"metilene\"];\n 2 -->|output| 13;\n 5 -->|output| 13;\n 3 -->|output| 13;\n 8 -->|output| 13;\n 7 -->|output| 13;\n 6 -->|output| 13;\n 14[\"MethylDackel\"];\n 11 -->|output| 14;\n 15[\"MethylDackel\"];\n 11 -->|output| 15;\n 16[\"Select last\"];\n 12 -->|outfile_replace| 16;\n 17[\"Select last\"];\n 15 -->|outFileExtractCpGFraction| 17;\n 18[\"computeMatrix\"];\n 16 -->|outfile| 18;\n 2 -->|output| 18;\n 19[\"Text reformatting\"];\n 17 -->|outfile| 19;\n 20[\"computeMatrix\"];\n 19 -->|outfile| 20;\n 2 -->|output| 20;\n 21[\"plotProfile\"];\n 20 -->|outFileName| 21;\n 5f1c4c17-572c-4f07-b82e-e2a2b468ae48[\"Output\\nplot_profile_tabular\"];\n 21 --> 5f1c4c17-572c-4f07-b82e-e2a2b468ae48;\n style 5f1c4c17-572c-4f07-b82e-e2a2b468ae48 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 0 -->|output| 9;\n 10[\"FastQC\"];\n 1 -->|output| 10;\n 11[\"bwameth\"];\n 0 -->|output| 11;\n 1 -->|output| 11;\n 12[\"Replace column\"];\n 3 -->|output| 12;\n 4 -->|output| 12;\n 13[\"metilene\"];\n 2 -->|output| 13;\n 5 -->|output| 13;\n 3 -->|output| 13;\n 8 -->|output| 13;\n 7 -->|output| 13;\n 6 -->|output| 13;\n 14[\"MethylDackel\"];\n 11 -->|output| 14;\n 15[\"MethylDackel\"];\n 11 -->|output| 15;\n 16[\"Select last\"];\n 12 -->|outfile_replace| 16;\n 17[\"Select last\"];\n 15 -->|outFileExtractCpGFraction| 17;\n 18[\"computeMatrix\"];\n 16 -->|outfile| 18;\n 2 -->|output| 18;\n 19[\"Text reformatting\"];\n 17 -->|outfile| 19;\n 20[\"computeMatrix\"];\n 19 -->|outfile| 20;\n 2 -->|output| 20;\n 21[\"plotProfile\"];\n 20 -->|outFileName| 21;\n c5b35dea-ecfd-4bc2-87db-780aaa72e039[\"Output\\nplot_profile_tabular\"];\n 21 --> c5b35dea-ecfd-4bc2-87db-780aaa72e039;\n style c5b35dea-ecfd-4bc2-87db-780aaa72e039 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:16 +0000",
"name": "Workflow Methylation Seq",
"outputs": [
{
@@ -246682,7 +220409,7 @@
{
"label": "plot_profile_tabular",
"output_name": "output_outFileNameData",
- "uuid": "5f1c4c17-572c-4f07-b82e-e2a2b468ae48"
+ "uuid": "c5b35dea-ecfd-4bc2-87db-780aaa72e039"
}
]
}
@@ -247215,9 +220942,9 @@
],
"dir": "topics/epigenetics/tutorials/hicexplorer",
"edam_operation": [
+ "Read mapping",
"Generation",
"Sequence alignment",
- "Read mapping",
"Genome indexing"
],
"edam_topic": [],
@@ -247239,7 +220966,7 @@
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
"mod_date": "2024-10-15",
- "pageviews": 10968,
+ "pageviews": 10995,
"pub_date": "2018-02-23",
"questions": [
"Why is a Hi-C analysis useful?",
@@ -247248,13 +220975,13 @@
],
"short_id": "T00141",
"short_tools": [
- "hicexplorer_hicfindtads",
"hicexplorer_hiccorrectmatrix",
- "hicexplorer_hicmergematrixbins",
- "hicexplorer_hicplotmatrix",
+ "hicexplorer_hicfindtads",
+ "bwa_mem",
"hicexplorer_hicbuildmatrix",
+ "hicexplorer_hicplotmatrix",
"hicexplorer_hicpca",
- "bwa_mem",
+ "hicexplorer_hicmergematrixbins",
"hicexplorer_hicplottads"
],
"slides": false,
@@ -247285,6 +221012,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -247340,10 +221071,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -247390,11 +221117,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -247439,6 +221161,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -247491,10 +221217,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -247543,16 +221265,6 @@
"state": "exact",
"version": "2.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.7.2+galaxy0",
- "3.7.5+galaxy1",
- "3.7.6+galaxy1",
- "3.7.5+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -247579,7 +221291,8 @@
"3.6+galaxy1",
"3.7.5+galaxy1",
"3.6+galaxy0",
- "3.7.5+galaxy0"
+ "3.7.5+galaxy0",
+ "3.7.6+galaxy1"
]
},
{
@@ -247612,6 +221325,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -247664,10 +221381,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -247716,16 +221429,6 @@
"state": "exact",
"version": "2.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.7.2+galaxy0",
- "3.7.6+galaxy1",
- "3.7.5+galaxy0",
- "3.7.5+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -247739,8 +221442,8 @@
"state": "inexact",
"versions": [
"3.7.2+galaxy0",
- "3.7.5+galaxy0",
- "3.7.5+galaxy1"
+ "3.7.5+galaxy1",
+ "3.7.5+galaxy0"
]
},
{
@@ -247748,8 +221451,9 @@
"state": "inexact",
"versions": [
"3.7.2+galaxy0",
- "3.7.5+galaxy0",
- "3.7.5+galaxy1"
+ "3.7.6+galaxy1",
+ "3.7.5+galaxy1",
+ "3.7.5+galaxy0"
]
},
{
@@ -247782,6 +221486,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -247834,10 +221542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -247886,10 +221590,6 @@
"state": "exact",
"version": "2.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -247915,8 +221615,9 @@
"3.4.3.0",
"3.6+galaxy1",
"3.7.5+galaxy0",
+ "3.7.5+galaxy1",
"3.6+galaxy0",
- "3.7.5+galaxy1"
+ "3.7.6+galaxy1"
]
},
{
@@ -247949,6 +221650,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -248001,10 +221706,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -248053,16 +221754,6 @@
"state": "exact",
"version": "2.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.7.2+galaxy0",
- "3.7.6+galaxy1",
- "3.7.5+galaxy0",
- "3.7.5+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -248075,8 +221766,8 @@
"state": "inexact",
"versions": [
"3.7.2+galaxy0",
- "3.7.5+galaxy0",
- "3.7.5+galaxy1"
+ "3.7.5+galaxy1",
+ "3.7.5+galaxy0"
]
},
{
@@ -248086,9 +221777,10 @@
"3.7.2+galaxy0",
"3.4.3.0",
"3.6+galaxy1",
- "3.6+galaxy0",
+ "3.7.5+galaxy1",
"3.7.5+galaxy0",
- "3.7.5+galaxy1"
+ "3.6+galaxy0",
+ "3.7.6+galaxy1"
]
},
{
@@ -248121,6 +221813,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -248173,10 +221869,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -248225,10 +221917,6 @@
"state": "exact",
"version": "2.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
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+ "pageviews": 2244,
"priority": 0,
"pub_date": "2024-05-10",
"questions": [
@@ -249833,10 +223128,10 @@
],
"short_id": "T00440",
"short_tools": [
- "iqtree",
- "fasttree",
+ "newick_display",
"rbc_mafft",
- "newick_display"
+ "iqtree",
+ "fasttree"
],
"slides": false,
"slides_recordings": false,
@@ -249904,6 +223199,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -249959,10 +223258,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -250009,11 +223304,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -250058,6 +223348,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -250112,10 +223406,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -250160,11 +223450,6 @@
"state": "exact",
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},
- {
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- "state": "exact",
- "version": "2.1.10+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -250211,157 +223496,7 @@
"state": "missing"
},
{
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- "state": "missing"
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- "state": "missing"
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- "state": "exact",
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- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
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- "1.5.5",
- "1.5.5.1"
- ]
- },
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- "server": "https://usegalaxy.cz/",
- "state": "exact",
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- {
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- "state": "exact",
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- "state": "exact",
- "version": "2.1.2+galaxy2"
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- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.1.2+galaxy2"
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- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -250386,7 +223521,8 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -250395,7 +223531,7 @@
{
"server": "https://galaxytrakr.org/",
"state": "exact",
- "version": "1.6+galaxy1"
+ "version": "2.1.2+galaxy2"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -250417,10 +223553,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -250451,21 +223583,165 @@
},
{
"server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "1.5.5.3",
+ "1.5.5.1",
+ "1.5.5"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "2.1.2+galaxy2"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
"state": "exact",
"version": "1.6+galaxy1"
},
{
- "server": "https://usegalaxy.cz/",
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
"state": "exact",
"version": "1.6+galaxy1"
},
{
- "server": "https://usegalaxy.eu",
+ "server": "https://usegalaxy.cz/",
"state": "exact",
"version": "1.6+galaxy1"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.6+galaxy1"
},
@@ -250514,6 +223790,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -250550,8 +223830,8 @@
"state": "inexact",
"versions": [
"7.221.3",
- "7.508+galaxy0",
- "7.475+galaxy0"
+ "7.475+galaxy0",
+ "7.508+galaxy0"
]
},
{
@@ -250574,10 +223854,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -250632,11 +223908,6 @@
"state": "exact",
"version": "7.508+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "7.508+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -250696,8 +223967,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 122,
- "visitors": 1604,
+ "visit_duration": 126,
+ "visitors": 1671,
"workflows": [
{
"creators": [
@@ -250774,7 +224045,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput FASTA Sequence File\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"MAFFT\"];\n 0 -->|output| 1;\n e5d56101-daff-420b-82e9-dc6cc923f7ab[\"Output\\noutputAlignment\"];\n 1 --> e5d56101-daff-420b-82e9-dc6cc923f7ab;\n style e5d56101-daff-420b-82e9-dc6cc923f7ab stroke:#2c3143,stroke-width:4px;\n 2[\"FASTTREE\"];\n 1 -->|outputAlignment| 2;\n 632ce28d-3086-490e-bd97-949eb2cb385a[\"Output\\noutput\"];\n 2 --> 632ce28d-3086-490e-bd97-949eb2cb385a;\n style 632ce28d-3086-490e-bd97-949eb2cb385a stroke:#2c3143,stroke-width:4px;\n 3[\"IQ-TREE\"];\n 1 -->|outputAlignment| 3;\n b8434b2b-2001-4b1a-bd06-faeab18519a4[\"Output\\ntreefile\"];\n 3 --> b8434b2b-2001-4b1a-bd06-faeab18519a4;\n style b8434b2b-2001-4b1a-bd06-faeab18519a4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Tree Building (imported from uploaded file)",
"outputs": [
{
@@ -251218,8 +224489,8 @@
"topic_3324"
],
"edam_operation": [
- "Sequence analysis",
- "Phylogenetic tree analysis"
+ "Phylogenetic tree analysis",
+ "Sequence analysis"
],
"edam_topic": [
"Genomics",
@@ -251249,7 +224520,7 @@
"Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
"Be able to read and interrogate a phylogeny encountered in the literature"
],
- "pageviews": 2183,
+ "pageviews": 2188,
"pub_date": "2022-03-16",
"questions": [
"What information can I get from a phylogenetic tree?",
@@ -251273,8 +224544,8 @@
],
"short_id": "T00144",
"short_tools": [
- "upload1",
"interactive_tool_rstudio",
+ "upload1",
"raxml"
],
"slides": false,
@@ -251317,6 +224588,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -251372,10 +224647,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -251422,11 +224693,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -251471,6 +224737,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -251523,10 +224793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -251567,10 +224833,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -251613,6 +224875,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -251666,10 +224932,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -251715,11 +224977,6 @@
"state": "exact",
"version": "8.2.12+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "8.2.12+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -251768,6 +225025,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -251821,10 +225082,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -251868,14 +225125,6 @@
"state": "exact",
"version": "8.2.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "8.2.12+galaxy0",
- "8.2.12+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -251924,6 +225173,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -251976,10 +225229,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -252020,10 +225269,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -252080,7 +225325,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 137,
- "visitors": 1466,
+ "visitors": 1471,
"workflows": [
{
"creators": [],
@@ -252151,7 +225396,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput alignment\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"RStudio\"];\n 2[\"Estimate phylogeny with RAxML\"];\n 0 -->|output| 2;\n 9f8ae577-c583-4a2d-b64d-14c25fb859d9[\"Output\\nBest-scoring ML Tree\"];\n 2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;\n style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;\n bdb8cf2f-b553-4a96-8b55-38b4b499ab88[\"Output\\nInfo\"];\n 2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;\n style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Mtb phylogeny",
"outputs": [
{
@@ -252649,9 +225894,9 @@
"topic_2885"
],
"edam_operation": [
+ "Phylogenetic tree visualisation",
"Antimicrobial resistance prediction",
"Variant calling",
- "Phylogenetic tree visualisation",
"Phylogenetic tree generation"
],
"edam_topic": [
@@ -252692,7 +225937,7 @@
"Identify transmission clusters based on SNP distances",
"Study the emergence and spread of drug resistance based on transmission analysis."
],
- "pageviews": 2625,
+ "pageviews": 2633,
"pub_date": "2022-03-16",
"requirements": [
{
@@ -252712,23 +225957,23 @@
],
"short_id": "T00145",
"short_tools": [
- "Grep1",
- "tp_easyjoin_tool",
+ "tp_sed_tool",
+ "collapse_dataset",
+ "snippy",
"bcftools_consensus",
- "tb_profiler_profile",
"tp_cat",
- "__MERGE_COLLECTION__",
- "snp_dists",
+ "tp_easyjoin_tool",
+ "samtools_view",
"addName",
- "tp_replace_in_line",
- "snippy",
- "collapse_dataset",
"trimmomatic",
- "upload1",
- "tp_grep_tool",
- "tp_sed_tool",
- "samtools_view",
+ "Grep1",
+ "snp_dists",
+ "__MERGE_COLLECTION__",
"snp_sites",
+ "tp_grep_tool",
+ "upload1",
+ "tb_profiler_profile",
+ "tp_replace_in_line",
"tb_variant_filter"
],
"slides": false,
@@ -252781,6 +226026,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -252836,10 +226085,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -252886,11 +226131,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -252935,6 +226175,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -252987,10 +226231,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -253031,10 +226271,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -253077,6 +226313,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -253129,10 +226369,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -253173,10 +226409,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -253219,6 +226451,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -253273,10 +226509,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -253325,11 +226557,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -253375,6 +226602,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -253429,10 +226660,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -253479,11 +226706,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -253529,6 +226751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -253583,10 +226809,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -253633,11 +226855,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -253683,6 +226900,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -253737,10 +226958,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -253787,11 +227004,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -253837,6 +227049,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -253891,10 +227107,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -253941,11 +227153,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -253991,6 +227198,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254047,10 +227258,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -254085,10 +227292,10 @@
"state": "inexact",
"versions": [
"1.9+galaxy2",
- "1.9+galaxy1",
- "1.10",
+ "1.9",
"1.4.0",
- "1.9"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -254101,18 +227308,13 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -254155,6 +227357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254213,10 +227419,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -254266,27 +227468,13 @@
"state": "exact",
"version": "1.9+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.15.1+galaxy3",
- "1.10+galaxy1",
- "1.9+galaxy1",
- "1.10",
- "1.15.1+galaxy0",
- "1.15.1+galaxy2",
- "1.15.1+galaxy4",
- "1.15.1+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -254300,12 +227488,12 @@
"versions": [
"1.15.1+galaxy3",
"1.10+galaxy1",
- "1.10",
- "1.4.0",
"1.9",
- "1.15.1+galaxy0",
+ "1.4.0",
+ "1.10",
+ "1.15.1+galaxy4",
"1.15.1+galaxy2",
- "1.15.1+galaxy4"
+ "1.15.1+galaxy0"
]
},
{
@@ -254338,6 +227526,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254362,8 +227554,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -254397,10 +227589,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -254452,11 +227640,6 @@
"state": "exact",
"version": "1.13+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.13+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -254502,6 +227685,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254535,8 +227722,8 @@
"state": "inexact",
"versions": [
"4.5.0+galaxy1",
- "4.5.0",
- "4.6.0+galaxy0"
+ "4.6.0+galaxy0",
+ "4.5.0"
]
},
{
@@ -254559,10 +227746,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -254608,13 +227791,6 @@
"state": "exact",
"version": "3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.6.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -254630,8 +227806,8 @@
"state": "inexact",
"versions": [
"4.5.0+galaxy1",
- "4.5.0",
- "4.6.0+galaxy0"
+ "4.6.0+galaxy0",
+ "4.5.0"
]
},
{
@@ -254664,6 +227840,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254717,10 +227897,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -254754,14 +227930,14 @@
"state": "inexact",
"versions": [
"4.5.0",
- "3.2+galaxy1",
- "4.4.5+galaxy0",
- "4.4.3+galaxy0",
"3.2",
- "4.3.6+galaxy2",
- "4.4.5+galaxy2",
"4.4.5+galaxy1",
- "4.3.6+galaxy1"
+ "4.3.6+galaxy1",
+ "4.4.3+galaxy0",
+ "3.2+galaxy1",
+ "4.3.6+galaxy2",
+ "4.4.5+galaxy0",
+ "4.4.5+galaxy2"
]
},
{
@@ -254774,17 +227950,12 @@
"state": "exact",
"version": "4.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "3.2+galaxy1",
- "3.2"
+ "3.2",
+ "3.2+galaxy1"
]
},
{
@@ -254827,6 +227998,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -254880,10 +228055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -254927,10 +228098,6 @@
"state": "exact",
"version": "0.6.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -254980,6 +228147,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255033,10 +228204,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -255082,10 +228249,6 @@
"state": "exact",
"version": "0.8.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -255131,6 +228294,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255184,10 +228351,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -255231,10 +228394,6 @@
"state": "exact",
"version": "2.5.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -255280,6 +228439,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255332,10 +228495,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -255382,10 +228541,6 @@
"state": "exact",
"version": "0.1.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -255431,6 +228586,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255483,10 +228642,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -255535,10 +228690,6 @@
"state": "exact",
"version": "0.3.5+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -255584,6 +228735,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255636,10 +228791,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -255685,10 +228836,6 @@
"state": "exact",
"version": "0.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -255738,6 +228885,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -255790,10 +228941,6 @@
"server": "http://galaxy.interactomix.com/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -258113,79 +231228,6 @@
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@@ -258277,8 +231319,8 @@
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@@ -258290,16 +231332,6 @@
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@@ -258311,79 +231343,6 @@
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@@ -258408,7 +231367,7 @@
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@@ -258488,16 +231447,6 @@
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@@ -258509,79 +231458,6 @@
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{
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"state": "exact",
@@ -260272,6 +232878,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
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{
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- "state": "missing"
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{
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"state": "exact",
@@ -260419,6 +233021,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -260471,10 +233077,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
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"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
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"state": "exact",
@@ -260566,6 +233164,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
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"state": "exact",
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},
- {
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- "state": "missing"
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{
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@@ -260812,7 +233406,7 @@
],
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- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Data management in Medicinal Chemistry workflow",
"outputs": [
{
@@ -261299,7 +233893,7 @@
"objectives": [
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],
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"Learn the FAIR principles",
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],
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@@ -261692,16 +234286,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-intro/tutorial.json",
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@@ -261732,68 +234316,6 @@
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}
],
"copyright": "\u00a9 Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors",
@@ -261833,7 +234355,7 @@
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"Connect different parts of the Research Object using identifiers"
],
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@@ -261942,8 +234464,8 @@
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@@ -262394,7 +234916,7 @@
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@@ -262467,7 +234989,7 @@
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@@ -262667,7 +235189,7 @@
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"To submit raw reads to ENA using FTP"
],
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@@ -262757,8 +235279,8 @@
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@@ -262950,7 +235472,7 @@
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],
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@@ -263047,8 +235569,8 @@
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@@ -263389,7 +235911,7 @@
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],
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{
@@ -263505,7 +236027,8 @@
"StellaEggels"
],
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- "nfdi4plants"
+ "nfdi4plants",
+ "dfg"
],
"reviewing": []
},
@@ -263610,6 +236133,9 @@
},
{
"avatar": "/training-material/shared/images/logo-dataplant.svg",
+ "funder_name": "DFG",
+ "funding_database": "dfg",
+ "funding_id": "442077441",
"id": "nfdi4plants",
"joined": "2024-07",
"members": [
@@ -263624,7 +236150,17 @@
"name": "DataPLANT (NFDI4Plants)",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
"short_name": "DataPLANT",
- "url": "https://training.galaxyproject.org/training-material/api/organisations/nfdi4plants.json"
+ "url": "https://training.galaxyproject.org/training-material/api/grants/nfdi4plants.json"
+ },
+ {
+ "avatar": "/training-material/shared/images/DFG_grant.png",
+ "github": false,
+ "id": "dfg",
+ "joined": "2024-12",
+ "name": "Deutsche Forschungsgemeinschaft",
+ "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dfg/",
+ "short_name": "DFG",
+ "url": "https://training.galaxyproject.org/training-material/api/organisations/dfg.json"
}
],
"dir": "topics/fair/tutorials/dataplant-arcs",
@@ -263656,8 +236192,8 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
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- "pageviews": 174864,
+ "mod_date": "2024-12-11",
+ "pageviews": 197838,
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@@ -263740,12 +236276,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/dataplant-arcs/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/dataplant-arcs/tutorial.json"
},
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},
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@@ -264429,7 +236965,7 @@
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],
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@@ -264786,7 +237322,7 @@
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],
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"Learn best practices in data management",
"Learn how to introduce computational reproducibility in your research"
],
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],
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"Generate a workflow test using Planemo",
"Understand how testing can be automated with GitHub Actions"
],
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@@ -265905,8 +238441,8 @@
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+ "visit_duration": 65,
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},
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@@ -267307,7 +239843,7 @@
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"Find out what the requirements are for submitting"
],
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@@ -267395,8 +239931,8 @@
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@@ -267701,7 +240237,7 @@
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],
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+ "visit_duration": 174,
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@@ -268131,7 +240667,7 @@
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],
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],
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@@ -268627,117 +241151,12 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "by-covid",
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
}
],
"dir": "topics/galaxy-interface/tutorials/workflow-automation",
"edam_operation": [
- "Variant classification",
- "Tree-based sequence alignment"
+ "Tree-based sequence alignment",
+ "Variant classification"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -268751,8 +241170,7 @@
"hands_on": true,
"id": "galaxy-interface/workflow-automation",
"inexact_supported_servers": [
- "MISSISSIPPI",
- "UseGalaxy.fr"
+ "MISSISSIPPI"
],
"js_requirements": {
"mathjax": null,
@@ -268770,7 +241188,7 @@
"Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
"Learn how to use Pangolin to assign annotated variants to lineages."
],
- "pageviews": 2948,
+ "pageviews": 2952,
"pub_date": "2021-06-08",
"questions": [
"How can I schedule and run tens or hundreds of Galaxy workflows easily?",
@@ -268802,11 +241220,11 @@
],
"short_id": "T00162",
"short_tools": [
+ "snpSift_filter",
+ "collapse_dataset",
"bcftools_consensus",
"pangolin",
- "compose_text_param",
- "snpSift_filter",
- "collapse_dataset"
+ "compose_text_param"
],
"slides": false,
"slides_recordings": false,
@@ -268839,11 +241257,6 @@
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -268869,6 +241282,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -268924,10 +241341,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -268974,11 +241387,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -269023,6 +241431,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -269081,10 +241493,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -269134,11 +241542,6 @@
"state": "exact",
"version": "1.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.10"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -269184,6 +241587,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -269236,10 +241643,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -269283,11 +241686,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -269332,6 +241730,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -269364,11 +241766,11 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
"3.0.3+galaxy0",
+ "4.1.1+galaxy0",
"4.0.5+galaxy0",
- "4.1.1+galaxy0"
+ "3.1.16+galaxy0",
+ "4.1.2+galaxy0"
]
},
{
@@ -269391,10 +241793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -269444,26 +241842,6 @@
"state": "exact",
"version": "2.3.8"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
- "4.0.5+galaxy0",
- "4.1.1+galaxy0",
- "4.3+galaxy2",
- "4.2+galaxy0",
- "4.3+galaxy1",
- "3.1.17+galaxy1",
- "3.1.19+galaxy0",
- "3.1.20+galaxy0",
- "3.1.11+galaxy0",
- "4.0.5+galaxy2",
- "3.1.4+galaxy1",
- "3.1.14+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -269508,6 +241886,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -269564,10 +241946,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -269612,11 +241990,6 @@
"state": "exact",
"version": "4.3+t.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -269662,6 +242035,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -269718,10 +242095,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -269771,14 +242144,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -269838,7 +242203,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 126,
- "visitors": 2392,
+ "visitors": 2396,
"workflows": [
{
"creators": [
@@ -269971,7 +242336,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Compose text parameter value\"];\n 1 -->|output| 3;\n 4[\"SnpSift Filter\"];\n 3 -->|out1| 4;\n 0 -->|output| 4;\n ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n 4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n 5[\"bcftools consensus\"];\n 4 -->|output| 5;\n 2 -->|output| 5;\n 9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n 5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n 6[\"Collapse Collection\"];\n 5 -->|output_file| 6;\n 1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n 6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n 7[\"Pangolin\"];\n 6 -->|output| 7;\n e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n 7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "vcf2lineage",
"outputs": [
{
@@ -270537,7 +242902,6 @@
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -270570,7 +242934,7 @@
"objectives": [
"Understanding, viewing and creating workflow reports"
],
- "pageviews": 927,
+ "pageviews": 930,
"pub_date": "2022-06-02",
"questions": [
"What are workflow reports?",
@@ -270593,14 +242957,14 @@
],
"short_id": "T00165",
"short_tools": [
- "datamash_ops",
+ "Cut1",
+ "csv_to_tabular",
+ "Grouping1",
"Remove beginning1",
+ "datamash_ops",
"ggplot2_point",
- "tp_sorted_uniq",
"upload1",
- "csv_to_tabular",
- "Grouping1",
- "Cut1"
+ "tp_sorted_uniq"
],
"slides": false,
"slides_recordings": false,
@@ -270612,11 +242976,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -270673,6 +243032,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -270728,10 +243091,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -270778,11 +243137,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -270827,6 +243181,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -270879,10 +243237,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -270923,10 +243277,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -270969,6 +243319,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -271021,10 +243375,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -271065,10 +243415,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -271111,6 +243457,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -271163,10 +243513,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -271207,10 +243553,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -271253,6 +243595,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -271305,10 +243651,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -271349,10 +243691,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -271395,6 +243733,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -271449,10 +243791,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -271499,11 +243837,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -271549,6 +243882,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -271606,10 +243943,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -271656,11 +243989,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -271706,6 +244034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -271764,10 +244096,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -271805,8 +244133,8 @@
"versions": [
"2.2.1+galaxy1",
"2.2.1+galaxy2",
- "2.2.1+galaxy0",
- "2.2.1"
+ "2.2.1",
+ "2.2.1+galaxy0"
]
},
{
@@ -271821,11 +244149,6 @@
"state": "exact",
"version": "3.3.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -271871,6 +244194,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -271923,10 +244250,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -271967,10 +244290,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -272027,8 +244346,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 175,
- "visitors": 651,
+ "visit_duration": 174,
+ "visitors": 654,
"workflows": [
{
"creators": [],
@@ -272099,7 +244418,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Convert CSV to tabular\"];\n 0 -->|output| 1;\n 2[\"Datamash\"];\n 1 -->|tabular| 2;\n 5fc8c705-b9e2-4008-aa85-e84504b8395f[\"Output\\ndatamash_output\"];\n 2 --> 5fc8c705-b9e2-4008-aa85-e84504b8395f;\n style 5fc8c705-b9e2-4008-aa85-e84504b8395f stroke:#2c3143,stroke-width:4px;\n 3[\"Remove beginning\"];\n 1 -->|tabular| 3;\n 4[\"Cut\"];\n 3 -->|out_file1| 4;\n 5[\"Group\"];\n 3 -->|out_file1| 5;\n 7e07839c-e8ca-4692-8b8e-6eb3607066de[\"Output\\ngroup1\"];\n 5 --> 7e07839c-e8ca-4692-8b8e-6eb3607066de;\n style 7e07839c-e8ca-4692-8b8e-6eb3607066de stroke:#2c3143,stroke-width:4px;\n 6[\"Group\"];\n 3 -->|out_file1| 6;\n 9cb98227-aa5b-4b77-933c-ffba1e98566e[\"Output\\ngroup2\"];\n 6 --> 9cb98227-aa5b-4b77-933c-ffba1e98566e;\n style 9cb98227-aa5b-4b77-933c-ffba1e98566e stroke:#2c3143,stroke-width:4px;\n 7[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 7;\n 8[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 8;\n 9[\"Unique\"];\n 4 -->|out_file1| 9;\n fc73409c-7878-4391-bc91-f99a5be0ba06[\"Output\\nunique_output\"];\n 9 --> fc73409c-7878-4391-bc91-f99a5be0ba06;\n style fc73409c-7878-4391-bc91-f99a5be0ba06 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
"outputs": [
{
@@ -272506,7 +244825,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Convert CSV to tabular\"];\n 0 -->|output| 1;\n 2[\"Datamash\"];\n 1 -->|tabular| 2;\n 5381f9b0-5170-484c-828e-4469ec27ab3e[\"Output\\ndatamash_output\"];\n 2 --> 5381f9b0-5170-484c-828e-4469ec27ab3e;\n style 5381f9b0-5170-484c-828e-4469ec27ab3e stroke:#2c3143,stroke-width:4px;\n 3[\"Remove beginning\"];\n 1 -->|tabular| 3;\n 4[\"Cut\"];\n 3 -->|out_file1| 4;\n 5[\"Group\"];\n 3 -->|out_file1| 5;\n 836a57b3-3657-435b-b396-869af7e2f35e[\"Output\\ngroup1\"];\n 5 --> 836a57b3-3657-435b-b396-869af7e2f35e;\n style 836a57b3-3657-435b-b396-869af7e2f35e stroke:#2c3143,stroke-width:4px;\n 6[\"Group\"];\n 3 -->|out_file1| 6;\n 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d[\"Output\\ngroup2\"];\n 6 --> 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d;\n style 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d stroke:#2c3143,stroke-width:4px;\n 7[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 7;\n bbbac6ca-64fb-46ad-8798-6c7c5369ccaf[\"Output\\nSepal Plot (PNG)\"];\n 7 --> bbbac6ca-64fb-46ad-8798-6c7c5369ccaf;\n style bbbac6ca-64fb-46ad-8798-6c7c5369ccaf stroke:#2c3143,stroke-width:4px;\n 8[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 8;\n 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9[\"Output\\nPetal Plot (PNG)\"];\n 8 --> 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9;\n style 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9 stroke:#2c3143,stroke-width:4px;\n 9[\"Unique\"];\n 4 -->|out_file1| 9;\n 6bcc2f96-255e-48f5-a37b-7d6a2c123493[\"Output\\nIris Species\"];\n 9 --> 6bcc2f96-255e-48f5-a37b-7d6a2c123493;\n style 6bcc2f96-255e-48f5-a37b-7d6a2c123493 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Training: Workflow Reports",
"outputs": [
{
@@ -272853,6 +245172,13 @@
"install_resolver_dependencies": true,
"install_tool_dependencies": true,
"tools": [
+ {
+ "name": "ena_webin_cli",
+ "owner": "ieguinoa",
+ "revisions": "7d751b5943b0",
+ "tool_panel_section_label": "Using Galaxy and Managing your Data",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "ena_upload",
"owner": "iuc",
@@ -272862,22 +245188,8 @@
}
]
},
- "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ena_upload\n owner: iuc\n revisions: 9e2df763086c\n tool_panel_section_label: Send Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+ "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ena_webin_cli\n owner: ieguinoa\n revisions: 7d751b5943b0\n tool_panel_section_label: Using Galaxy and Managing your Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ena_upload\n owner: iuc\n revisions: 9e2df763086c\n tool_panel_section_label: Send Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json",
- "contributions": {
- "authorship": [
- "roncoronimiguel",
- "bedroesb",
- "B0r1sD"
- ],
- "reviewing": [
- "bedroesb",
- "hexylena",
- "shiltemann",
- "bgruening",
- "beatrizserrano"
- ]
- },
"contributors": [
{
"email": "miguel.roncoroni@elixir-belgium.org",
@@ -272919,125 +245231,6 @@
"name": "Boris Depoortere",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/B0r1sD/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/B0r1sD.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "be",
- "email": "bert.droesbeke@vib.be",
- "id": "bedroesb",
- "joined": "2019-12",
- "matrix": "bedroesb:matrix.org",
- "name": "Bert Droesbeke",
- "orcid": "0000-0003-0522-5674",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bedroesb/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bedroesb.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "beatrizserrano.galaxy@gmail.com",
- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
}
],
"dir": "topics/galaxy-interface/tutorials/upload-data-to-ena",
@@ -273048,7 +245241,9 @@
"feedback_number": 0,
"hands_on": true,
"id": "galaxy-interface/upload-data-to-ena",
- "inexact_supported_servers": [],
+ "inexact_supported_servers": [
+ "UseGalaxy.be"
+ ],
"js_requirements": {
"mathjax": null,
"mermaid": false
@@ -273063,12 +245258,12 @@
"layout": "tutorial_hands_on",
"level": "Intermediate",
"license": "CC-BY-4.0",
- "mod_date": "2024-04-04",
+ "mod_date": "2024-12-11",
"objectives": [
"Submit raw sequencing reads and metadata to ENA's test server",
"Submit consensus sequence and metadata to ENA's test server"
],
- "pageviews": 5088291,
+ "pageviews": 5111269,
"pub_date": "2021-08-10",
"questions": [
"How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -273092,13 +245287,19 @@
"short_id": "T00159",
"short_tools": [
"ena_upload",
- "ena_webin_cli"
+ "ena_consensus_submit"
],
"slides": true,
"slides_recordings": false,
"supported_servers": {
"exact": [],
- "inexact": []
+ "inexact": [
+ {
+ "name": "UseGalaxy.be",
+ "url": "https://usegalaxy.be/",
+ "usegalaxy": false
+ }
+ ]
},
"supported_servers_matrix": {
"servers": [
@@ -273122,6 +245323,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -273177,10 +245382,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -273227,11 +245428,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -273254,7 +245450,7 @@
],
"tools": [
{
- "id": "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_webin_cli/7d751b5943b0",
+ "id": "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_consensus_submit/4.3.0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -273276,6 +245472,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -273328,10 +245528,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -273362,7 +245558,8 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "missing"
+ "state": "exact",
+ "version": "4.3.0"
},
{
"server": "https://usegalaxy.cz/",
@@ -273372,10 +245569,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -273393,7 +245586,7 @@
"state": "missing"
}
],
- "version": "7d751b5943b0"
+ "version": "4.3.0"
},
{
"id": "toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2",
@@ -273418,6 +245611,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -273470,10 +245667,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -273509,9 +245702,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1"
]
},
@@ -273527,23 +245720,6 @@
"state": "exact",
"version": "0.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.7.3+galaxy1",
- "0.5.3",
- "0.3.1",
- "0.7.1+galaxy1",
- "0.6.1",
- "0.3.3",
- "0.6.3+galaxy0",
- "0.4.3",
- "0.6.0",
- "0.4.1",
- "0.7.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -273560,8 +245736,8 @@
"0.5.3",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
+ "0.3.3",
"0.4.3",
"0.6.0"
]
@@ -273596,6 +245772,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -273648,10 +245828,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -273687,9 +245863,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1"
]
},
@@ -273705,34 +245881,17 @@
"state": "inexact",
"versions": [
"0.7.3+galaxy1",
+ "0.3.1",
"0.3",
"0.5.3",
- "0.3.1",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
- "0.3.2",
- "0.4.3",
- "0.6.0",
- "0.4.1"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.7.3+galaxy1",
- "0.5.3",
- "0.3.1",
- "0.7.1+galaxy1",
- "0.6.1",
"0.3.3",
- "0.6.3+galaxy0",
"0.4.3",
"0.6.0",
- "0.4.1",
- "0.7.1+galaxy0"
+ "0.3.2",
+ "0.4.1"
]
},
{
@@ -273751,8 +245910,8 @@
"0.5.3",
"0.7.1+galaxy1",
"0.6.1",
- "0.3.3",
"0.6.3+galaxy0",
+ "0.3.3",
"0.4.3",
"0.6.0"
]
@@ -273773,7 +245932,7 @@
"time_estimation": "1h",
"title": "Submitting sequence data to ENA",
"tools": [
- "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_webin_cli/7d751b5943b0",
+ "toolshed.g2.bx.psu.edu/repos/ieguinoa/ena_webin_cli/ena_consensus_submit/4.3.0",
"toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.3.2",
"toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.7.1"
],
@@ -273792,12 +245951,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-data-to-ena/tutorial.json"
},
- "version": 9,
+ "version": 10,
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 238,
- "visitors": 1918758,
+ "visit_duration": 237,
+ "visitors": 1928826,
"workflows": [
{
"creators": [],
@@ -273821,7 +245980,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"ENA Upload tool\"];\n 1[\"ENA Upload tool\"];",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN_ENA_upload_workflow",
"outputs": [
{
@@ -273948,19 +246107,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-editor/tutorial.json",
- "contributions": {
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- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "lecorguille",
- "bgruening",
- "davelopez",
- "nsoranzo"
- ]
- },
"contributors": [
{
"id": "mvdbeek",
@@ -273968,135 +246114,6 @@
"name": "Marius van den Beek",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
- },
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
- "former_affiliations": [
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- "avans-atgm",
- "uni-freiburg"
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- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- {
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- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
- },
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- "eosc-life",
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "id": "davelopez",
- "joined": "2021-10",
- "name": "David L\u00f3pez",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davelopez/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/davelopez.json"
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- "elixir-europe"
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- "elixir_node": "uk",
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- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
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- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
}
],
"dir": "topics/galaxy-interface/tutorials/workflow-editor",
@@ -274107,7 +246124,6 @@
"UseGalaxy.be",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -274134,7 +246150,7 @@
"Understand key aspects of workflows",
"Create clean, non-repetitive workflows"
],
- "pageviews": 6098,
+ "pageviews": 6132,
"pub_date": "2020-07-17",
"questions": [
"How can you construct Galaxy workflows from scratch?",
@@ -274146,9 +246162,9 @@
],
"short_id": "T00163",
"short_tools": [
- "tp_tac",
"Show beginning1",
- "Paste1"
+ "Paste1",
+ "tp_tac"
],
"slides": false,
"slides_recordings": false,
@@ -274175,11 +246191,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -274226,6 +246237,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -274281,10 +246296,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -274331,11 +246342,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -274381,145 +246387,7 @@
"state": "local"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
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- "state": "local"
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- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
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- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "local"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "local"
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- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "local"
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- {
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- "state": "local"
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- "state": "missing"
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- "state": "missing"
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- "state": "local"
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- "state": "local"
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- "state": "local"
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- "state": "local"
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- {
- "server": "https://usegalaxy.be/",
- "state": "local"
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- {
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- "state": "local"
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- {
- "server": "https://usegalaxy.eu",
- "state": "local"
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- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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- {
- "server": "https://usegalaxy.no/",
- "state": "local"
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- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "local"
- }
- ],
- "version": "local"
- },
- {
- "id": "Show beginning1",
- "servers": [
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- "state": "local"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
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- "state": "missing"
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- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -274552,7 +246420,7 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -274574,10 +246442,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -274619,7 +246483,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Show beginning1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -274664,6 +246662,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -274718,10 +246720,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -274768,11 +246766,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -274828,7 +246821,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 180,
- "visitors": 4818,
+ "visitors": 4845,
"workflows": [
{
"creators": [],
@@ -274900,7 +246893,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Reverse dataset\"];\n 0 -->|output| 1;\n 2[\"Select first lines\"];\n 1 -->|outfile| 2;\n daf1abd9-a5c8-4b25-add1-5475e594f187[\"Output\\nFirst lines\"];\n 2 --> daf1abd9-a5c8-4b25-add1-5475e594f187;\n style daf1abd9-a5c8-4b25-add1-5475e594f187 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Tutorial workflow",
"outputs": [
{
@@ -275082,7 +247075,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\ud83d\udee0\ufe0f Subworkflow\\nworkflow 1\"];\n style 1 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 1;\n 88160926-01a6-4903-8737-1f3d65449e12[\"Output\\nFirst lines\"];\n 1 --> 88160926-01a6-4903-8737-1f3d65449e12;\n style 88160926-01a6-4903-8737-1f3d65449e12 stroke:#2c3143,stroke-width:4px;\n 2[\"\ud83d\udee0\ufe0f Subworkflow\\nworkflow 2\"];\n style 2 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 2;\n f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba[\"Output\\nFirst lines\"];\n 2 --> f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba;\n style f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba stroke:#2c3143,stroke-width:4px;\n 3[\"Paste\"];\n 1 -->|First lines| 3;\n 2 -->|First lines| 3;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Subworkflow",
"outputs": [
{
@@ -275793,8 +247786,8 @@
],
"short_id": "T00152",
"short_tools": [
- "intermine",
- "galaxy_intermine_exchange"
+ "galaxy_intermine_exchange",
+ "intermine"
],
"slides": false,
"slides_recordings": false,
@@ -275856,6 +247849,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -275911,10 +247908,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -275961,11 +247954,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -276011,147 +247999,9 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "local"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "local"
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- {
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- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
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- "server": "https://usegalaxy.no/",
- "state": "local"
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- "server": "https://usegalaxy.org",
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- "server": "https://usegalaxy.org.au",
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- "version": "local"
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- {
- "server": "http://smile.hku.hk/SARGs",
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- "state": "missing"
- },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -276170,11 +248020,11 @@
},
{
"server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
+ "state": "local"
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
+ "state": "local"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -276202,10 +248052,144 @@
},
{
"server": "http://galaxy.interactomix.com/",
+ "state": "local"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -276251,10 +248235,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -276369,7 +248349,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Create InterMine Interchange\"];\n 0 -->|output| 1;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Intermine import/export",
"outputs": [
{
@@ -276491,18 +248471,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json",
- "contributions": {
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- "mvdbeek",
- "hexylena"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "mvdbeek",
- "bgruening"
- ]
- },
"contributors": [
{
"id": "mvdbeek",
@@ -276539,106 +248507,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "id": "mvdbeek",
- "joined": "2018-06",
- "name": "Marius van den Beek",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
- },
- {
- "affiliations": [
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/galaxy-interface/tutorials/workflow-parameters",
@@ -276650,7 +248518,6 @@
"UseGalaxy.be",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -276676,7 +248543,7 @@
"objectives": [
"Learn how to use Workflow Parameters to improve your Workflows"
],
- "pageviews": 2182,
+ "pageviews": 2187,
"pub_date": "2019-06-27",
"questions": [
"What are Workflow Parameters",
@@ -276735,11 +248602,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -276786,6 +248648,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -276841,10 +248707,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -276891,11 +248753,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -276940,6 +248797,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -276994,10 +248855,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -277044,11 +248901,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -277101,8 +248953,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 133,
- "visitors": 1686,
+ "visit_duration": 132,
+ "visitors": 1691,
"workflows": [
{
"creators": [],
@@ -277154,7 +249006,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Select first\"];\n 0 -->|output| 1;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Select First N Lines",
"outputs": [
{
@@ -277268,20 +249120,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/tutorial.json",
- "contributions": {
- "authorship": [
- "avani-k",
- "bethsheets",
- "coverbeck",
- "afgane"
- ],
- "reviewing": [
- "hexylena",
- "avani-k",
- "bgruening",
- "shiltemann"
- ]
- },
"contributors": [
{
"email": "akhadilk@ucsc.edu",
@@ -277313,107 +249151,6 @@
"name": "Enis Afgan",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "email": "akhadilk@ucsc.edu",
- "id": "avani-k",
- "joined": "2021-12",
- "name": "Avani Khadilkar",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avani-k/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/avani-k.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/galaxy-interface/tutorials/galaxy-on-dockstore",
@@ -277446,7 +249183,7 @@
"Getting started with Galaxy workflows on Dockstore",
"Register your Galaxy workflow on Dockstore"
],
- "pageviews": 4343099,
+ "pageviews": 4366069,
"pub_date": "2022-01-14",
"short_id": "S00061",
"short_tools": [],
@@ -277513,7 +249250,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 150,
- "visitors": 1690942
+ "visitors": 1700989
},
{
"admin_install": {
@@ -277574,19 +249311,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: ddf54b12c295\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqtofasta\n owner: devteam\n revisions: 297962e79f39\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jq\n owner: iuc\n revisions: 5ff75eb1a893\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n owner: iuc\n revisions: 2a3a00c1fa0a\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n owner: iuc\n revisions: 69ebb7f46e45\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n owner: iuc\n revisions: 83c7d564b128\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
- "contributions": {
- "authorship": [
- "jontrow",
- "RareSeas"
- ],
- "reviewing": [
- "shiltemann",
- "mtekman",
- "hexylena",
- "bgruening",
- "natefoo"
- ]
- },
"contributors": [
{
"github": false,
@@ -277602,125 +249326,6 @@
"name": "Adelaide Rhodes",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/RareSeas/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/RareSeas.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
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- "twitter": "natefoo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
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"Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
"Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
],
- "pageviews": 5424204,
+ "pageviews": 5447176,
"pub_date": "2021-05-31",
"questions": [
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],
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"short_tools": [
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- "tp_cat",
- "fastq_dump",
- "fasterq_dump",
+ "jq",
"query_tabular",
"fastq_to_fasta_python",
- "jq"
+ "tp_cat",
+ "fasterq_dump",
+ "snpeff_sars_cov_2",
+ "fastq_dump"
],
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"slides_recordings": [
@@ -277872,6 +249477,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -277927,10 +249536,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
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"url": "https://usegalaxy.eu",
"usegalaxy": true
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -278080,10 +249684,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -278130,11 +249730,6 @@
"state": "exact",
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},
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- "version": "0.1.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -278180,6 +249775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -278233,10 +249832,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -278280,10 +249875,6 @@
"state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -278329,6 +249920,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -278381,10 +249976,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "exact",
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{
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"state": "exact",
@@ -278478,6 +250064,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -278586,18 +250172,6 @@
"state": "exact",
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- "3.0.1"
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{
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"state": "exact",
@@ -278643,6 +250217,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -278696,10 +250274,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "exact",
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- "version": "4.5covid19"
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{
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"state": "exact",
@@ -278794,6 +250363,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -278894,16 +250463,16 @@
"state": "inexact",
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+ "2.10.7+galaxy1",
"2.10.4",
"2.10.4+galaxy1",
- "2.10.7+galaxy1",
- "3.0.5+galaxy3",
- "2.10.4+galaxy2",
"2.10.8+galaxy0",
- "2.10.7+galaxy0",
+ "2.10.4+galaxy2",
"3.0.5+galaxy0",
"2.10.7+galaxy2",
- "3.0.3+galaxy0"
+ "2.10.7+galaxy0",
+ "3.0.3+galaxy0",
+ "3.0.5+galaxy3"
]
},
{
@@ -278911,11 +250480,6 @@
"state": "exact",
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},
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- "version": "2.11.0+galaxy0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -278963,6 +250527,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -279021,10 +250589,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -279068,16 +250632,16 @@
"2.9.1.3",
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"2.10.4",
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"2.8.0",
"2.10.4+galaxy1",
- "3.0.3+galaxy0",
- "2.10.8+galaxy0",
- "3.0.5+galaxy3",
- "1.2.5",
+ "2.10.7+galaxy1",
+ "2.10.7+galaxy2",
"2.10.7+galaxy0",
+ "1.2.5",
+ "2.10.8+galaxy0",
"3.0.5+galaxy0",
- "2.10.7+galaxy2"
+ "3.0.5+galaxy3",
+ "3.0.3+galaxy0"
]
},
{
@@ -279085,22 +250649,17 @@
"state": "inexact",
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"3.0.5+galaxy0",
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- "3.0.8+galaxy0",
- "3.1.0+galaxy0",
- "3.1.0+galaxy1",
+ "3.0.5+galaxy3",
+ "3.0.3+galaxy0",
"3.0.8+galaxy1",
- "3.1.1+galaxy1"
+ "3.1.1+galaxy1",
+ "3.1.0+galaxy1",
+ "3.1.0+galaxy0",
+ "3.0.8+galaxy0",
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]
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{
"server": "https://usegalaxy.no/",
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@@ -279160,8 +250719,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 260,
- "visitors": 2019505
+ "visit_duration": 259,
+ "visitors": 2029550
},
{
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@@ -279172,23 +250731,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/tutorial.json",
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- "tnabtaf",
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- "shiltemann",
- "bebatut",
- "gallardoalba",
- "tnabtaf",
- "willdurand"
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"contributors": [
{
"id": "pajanne",
@@ -279245,140 +250787,6 @@
"orcid": "0000-0003-3803-468X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "gallantries",
- "by-covid",
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- "elixir-converge"
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- "name": "Helena Rasche",
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- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
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- "elixir_node": "nl",
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- "fediverse": "https://mstdn.science/@shiltemann",
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- "fediverse": "https://piaille.fr/@bebatut",
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- "elixir-europe"
- ],
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- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
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- "joined": "2017-09",
- "name": "Dave Clements",
- "orcid": "0000-0002-9970-6657",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
- },
- {
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- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
}
],
"dir": "topics/galaxy-interface/tutorials/get-data",
@@ -279405,7 +250813,7 @@
"logo": "GTN",
"mod_date": "2022-10-18",
"objectives": null,
- "pageviews": 6179079,
+ "pageviews": 6202049,
"pub_date": "2017-05-24",
"questions": [
"How do I get my data into Galaxy?",
@@ -279482,7 +250890,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 153,
- "visitors": 2242499,
+ "visitors": 2253323,
"zenodo_link": ""
},
{
@@ -279957,7 +251365,7 @@
"objectives": [
"Gain understanding on navigating and manipulating histories"
],
- "pageviews": 5782,
+ "pageviews": 5801,
"pub_date": "2017-02-20",
"questions": [
"How do Galaxy histories work?"
@@ -280059,8 +251467,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 169,
- "visitors": 4454,
+ "visit_duration": 168,
+ "visitors": 4471,
"zenodo_link": ""
},
{
@@ -280072,17 +251480,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/download-delete-data/tutorial.json",
- "contributions": {
- "authorship": [
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- "hexylena"
- ],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "bgruening"
- ]
- },
"contributors": [
{
"elixir_node": "au",
@@ -280123,99 +251520,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "uni-freiburg"
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- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "nfdi4plants",
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"visit_duration": 133,
- "visitors": 1711,
+ "visitors": 1715,
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@@ -281827,18 +252715,6 @@
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"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json",
- "contributions": {
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- "reviewing": [
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- "shiltemann",
- "bebatut",
- "lecorguille",
- "bgruening"
- ]
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"contributors": [
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@@ -281868,136 +252744,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "gallantries",
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- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "nfdi4plants",
- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
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- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
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- "linkedin": "shiltemann",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
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- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
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- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/galaxy-interface/tutorials/name-tags",
@@ -282029,7 +252775,7 @@
"Learn how to set name tags",
"Learn how they are propagated"
],
- "pageviews": 1895,
+ "pageviews": 1900,
"pub_date": "2019-04-08",
"questions": [
"What are name tags or hash tags?",
@@ -282105,8 +252851,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 171,
- "visitors": 1379,
+ "visit_duration": 172,
+ "visitors": 1384,
"zenodo_link": ""
},
{
@@ -282459,7 +253205,7 @@
"objectives": [
"Launch RStudio in Galaxy"
],
- "pageviews": 7078,
+ "pageviews": 7088,
"pub_date": "2019-10-08",
"questions": [
"How can I manipulate data using R in Galaxy?"
@@ -282518,6 +253264,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -282573,10 +253323,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -282623,11 +253369,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -282672,6 +253413,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -282724,10 +253469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -282768,10 +253509,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -282822,7 +253559,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 125,
- "visitors": 4422,
+ "visitors": 4431,
"zenodo_link": ""
},
{
@@ -282863,25 +253600,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/collections/tutorial.json",
- "contributions": {
- "authorship": [
- "nekrut"
- ],
- "reviewing": [
- "bgruening",
- "hexylena",
- "shiltemann",
- "nekrut",
- "nsoranzo",
- "bebatut",
- "beatrizserrano",
- "tnabtaf",
- "willdurand",
- "njall",
- "mblue9",
- "TheKharleeci"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -282890,206 +253608,13 @@
"name": "Anton Nekrutenko",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
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- "deNBI",
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- "elixir-converge",
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "elixir-converge"
- ],
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
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- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
- {
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- "earlham",
- "elixir-europe"
- ],
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- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
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- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "beatrizserrano.galaxy@gmail.com",
- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
- },
- {
- "id": "tnabtaf",
- "joined": "2017-09",
- "name": "Dave Clements",
- "orcid": "0000-0002-9970-6657",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
- },
- {
- "id": "willdurand",
- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
- },
- {
- "id": "mblue9",
- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
- },
- {
- "id": "TheKharleeci",
- "name": "TheKharleeci",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TheKharleeci/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/TheKharleeci.json"
}
],
"dir": "topics/galaxy-interface/tutorials/collections",
"edam_operation": [
+ "Read mapping",
"Generation",
"Sequence alignment",
- "Read mapping",
"Genome indexing"
],
"edam_topic": [],
@@ -283107,7 +253632,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no"
],
"js_requirements": {
@@ -283127,7 +253651,7 @@
"objectives": [
"Understand and master dataset collections"
],
- "pageviews": 17874,
+ "pageviews": 17934,
"pub_date": "2016-09-30",
"questions": [
"How to manipulate large numbers of datasets at once?"
@@ -283166,8 +253690,8 @@
],
"short_id": "T00146",
"short_tools": [
- "collapse_dataset",
"snpSift_extractFields",
+ "collapse_dataset",
"lofreq_call",
"bwa_mem"
],
@@ -283213,11 +253737,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -283247,6 +253766,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -283302,10 +253825,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -283352,11 +253871,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -283401,6 +253915,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -283458,10 +253976,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -283509,11 +254023,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -283562,6 +254071,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -283615,10 +254128,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -283656,8 +254165,8 @@
"versions": [
"2.1.3.1+galaxy2",
"2.1.3.1+galaxy1",
- "2.1.5+galaxy0",
- "2.1.3.1+galaxy0"
+ "2.1.3.1+galaxy0",
+ "2.1.5+galaxy0"
]
},
{
@@ -283672,11 +254181,6 @@
"state": "exact",
"version": "2.1.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -283722,6 +254226,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -283776,10 +254284,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -283824,11 +254328,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
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- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -283874,6 +254373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -283899,8 +254402,8 @@
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -283934,10 +254437,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -283987,21 +254486,13 @@
"state": "exact",
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},
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
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{
@@ -284054,8 +254545,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 182,
- "visitors": 12816,
+ "visit_duration": 181,
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"zenodo_link": "https://doi.org/10.5281/zenodo.5119008"
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{
@@ -284067,21 +254558,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json",
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- "bernt-matthias"
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"contributors": [
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@@ -284089,172 +254565,6 @@
"name": "Marius van den Beek",
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"url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
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@@ -284285,7 +254595,7 @@
"Learn how to set group tags",
"Learn how to select group tags in tools"
],
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+ "pageviews": 3416,
"pub_date": "2019-03-06",
"questions": [
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@@ -284361,8 +254671,8 @@
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"video_view": 0,
- "visit_duration": 198,
- "visitors": 2491,
+ "visit_duration": 200,
+ "visitors": 2495,
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},
{
@@ -284374,22 +254684,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json",
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- "bebatut"
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"contributors": [
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@@ -284430,168 +254724,6 @@
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}
],
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@@ -284620,7 +254752,7 @@
"objectives": [
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],
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+ "pageviews": 874,
"pub_date": "2018-05-25",
"questions": [
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@@ -284718,8 +254850,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 345,
- "visitors": 641,
+ "visit_duration": 343,
+ "visitors": 643,
"zenodo_link": ""
},
{
@@ -284869,7 +255001,7 @@
"Learn how to utilize external tools to make high resolution images of your Workflow",
"Learn how to compress high resolution Workflow images to share them in the web"
],
- "pageviews": 146,
+ "pageviews": 148,
"pub_date": "2024-02-05",
"questions": [
"How can I print or screenshot my Workflow in high resolution for a poster or presentation?",
@@ -284937,6 +255069,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -284992,10 +255128,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -285042,11 +255174,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -285091,6 +255218,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -285143,10 +255274,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -285196,10 +255323,6 @@
"state": "exact",
"version": "1.3.40+galaxy0"
},
- {
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- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -285254,8 +255377,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 166,
- "visitors": 115
+ "visit_duration": 163,
+ "visitors": 117
},
{
"admin_install": {
@@ -285266,17 +255389,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json",
- "contributions": {
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- ],
- "reviewing": [
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- "shiltemann",
- "mvdbeek"
- ]
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"contributors": [
{
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@@ -285314,75 +255426,6 @@
"name": "Anton Nekrutenko",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
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- "matrix": "hexylena:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
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- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "name": "Marius van den Beek",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
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}
],
"dir": "topics/galaxy-interface/tutorials/search",
@@ -285414,7 +255457,7 @@
"objectives": [
"Feel confident in searching your history"
],
- "pageviews": 551,
+ "pageviews": 552,
"pub_date": "2020-07-15",
"questions": [
"How can you find your datasets?",
@@ -285486,8 +255529,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 146,
- "visitors": 348,
+ "visit_duration": 145,
+ "visitors": 349,
"zenodo_link": ""
},
{
@@ -285521,25 +255564,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
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- "slugger70"
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"contributors": [
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@@ -285570,202 +255594,6 @@
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- "fediverse_flavor": "mastodon",
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- "bio": "Researcher at Erasmus Medical Center",
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- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "linkedin": "shiltemann",
- "location": {
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "contact_for_training": true,
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- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
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- "location": {
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- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "contact_for_training": true,
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- "fediverse": "https://genomic.social/@abretaud",
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- "fediverse": "https://mstdn.science/@nsoranzo",
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- "matrix": "nsoranzo:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
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- "id": "slugger70",
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}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
@@ -285776,9 +255604,9 @@
"topic_0080"
],
"edam_operation": [
- "Coding region prediction",
"Genome annotation",
"Genome visualisation",
+ "Coding region prediction",
"Gene prediction"
],
"edam_topic": [
@@ -285810,7 +255638,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -285831,7 +255658,7 @@
"Annotate genome with Prokka",
"View annotations in JBrowse"
],
- "pageviews": 6207673,
+ "pageviews": 6230726,
"pub_date": "2018-03-06",
"questions": [
"How can we annotate a bacterial genome?",
@@ -285853,8 +255680,8 @@
],
"short_id": "T00168",
"short_tools": [
- "prokka",
- "jbrowse"
+ "jbrowse",
+ "prokka"
],
"slides": true,
"slides_recordings": [
@@ -285911,11 +255738,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -285950,6 +255772,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -286005,10 +255831,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -286055,11 +255877,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -286105,172 +255922,7 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -286372,7 +256020,7 @@
{
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+ "version": "1.14.5"
},
{
"server": "https://usegalaxy.cz/",
@@ -286384,10 +256032,165 @@
{
"server": "https://usegalaxy.eu",
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+ "state": "inexact",
+ "versions": [
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+ ]
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+ "server": "https://usegalaxy.org",
+ "state": "exact",
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "inexact",
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+ ]
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+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
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+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
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+ "state": "missing"
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+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ "state": "inexact",
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+ "state": "missing"
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+ "server": "https://galaxy.bio.di.uminho.pt/",
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+ "server": "https://usegalaxy.be/",
+ "state": "exact",
"version": "1.14.5+galaxy0"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "1.14.6+galaxy1"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.14.5+galaxy0"
},
@@ -286406,8 +256209,8 @@
"state": "inexact",
"versions": [
"1.14.6+galaxy1",
- "1.14.5",
"1.12.0",
+ "1.14.5",
"1.14.6+galaxy0"
]
},
@@ -286441,6 +256244,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -286496,10 +256303,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -286535,23 +256338,23 @@
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"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
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+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -286564,11 +256367,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -286627,7 +256425,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 262,
- "visitors": 2258940,
+ "visitors": 2269815,
"workflows": [
{
"creators": [
@@ -286758,7 +256556,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Prokka\"];\n 0 -->|output| 1;\n a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n 1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n 2[\"JBrowse\"];\n 1 -->|out_fna| 2;\n 1 -->|out_gff| 2;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome Annotation with Prokka ",
"outputs": [
{
@@ -287281,7 +257079,7 @@
"Learn how to manually refine genome annotations within Apollo",
"Export refined genome annotations"
],
- "pageviews": 5401704,
+ "pageviews": 5424682,
"pub_date": "2021-06-04",
"questions": [
"How to visualize your genome after automated annotations have been performed?",
@@ -287322,10 +257120,10 @@
"short_id": "T00169",
"short_tools": [
"create_account",
- "jbrowse",
- "iframe",
"create_or_update",
- "list_organism"
+ "list_organism",
+ "jbrowse",
+ "iframe"
],
"slides": true,
"slides_recordings": [
@@ -287385,6 +257183,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -287440,10 +257242,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -287490,11 +257288,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -287539,6 +257332,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -287591,10 +257388,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -287639,10 +257432,6 @@
"state": "exact",
"version": "3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -287688,6 +257477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -287740,10 +257533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -287790,10 +257579,6 @@
"4.2.13+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -287837,6 +257622,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -287889,10 +257678,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -287937,10 +257722,6 @@
"state": "exact",
"version": "4.2.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -287984,6 +257765,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -288036,10 +257821,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -288084,10 +257865,6 @@
"state": "exact",
"version": "3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -288133,6 +257910,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -288188,10 +257969,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -288227,23 +258004,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -288256,11 +258033,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -288322,7 +258094,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 313,
- "visitors": 2014123,
+ "visitors": 2024178,
"workflows": [
{
"creators": [],
@@ -288513,7 +258285,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Register Account\"];\n 5[\"List Organisms\"];\n 6[\"JBrowse\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 3 -->|output| 6;\n 2 -->|output| 6;\n 7[\"Create or Update Organism\"];\n 6 -->|output| 7;\n 8[\"Annotate\"];\n 7 -->|output| 8;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Apollo Load Test",
"outputs": [
{
@@ -289327,17 +259099,16 @@
],
"dir": "topics/genome-annotation/tutorials/repeatmasker",
"edam_operation": [
- "Genome annotation",
"Editing",
- "RNA-Seq analysis",
+ "Repeat sequence detection",
+ "Genome annotation",
"Mapping",
- "Repeat sequence detection"
+ "RNA-Seq analysis"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -289370,7 +259141,7 @@
"objectives": [
"Use Red and RepeatMasker to soft-mask a newly assembled genome"
],
- "pageviews": 10206,
+ "pageviews": 10253,
"priority": 1,
"pub_date": "2021-11-29",
"questions": [
@@ -289425,11 +259196,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -289465,6 +259231,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -289520,10 +259290,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -289570,11 +259336,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -289619,6 +259380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -289671,10 +259436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -289707,9 +259468,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "4.0.9",
"4.0.7+galaxy2",
- "4.1.2-p1+galaxy0"
+ "4.1.2-p1+galaxy0",
+ "4.0.9"
]
},
{
@@ -289722,17 +259483,12 @@
"state": "exact",
"version": "4.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "4.0.9",
"4.1.2-p1+galaxy0",
+ "4.0.9",
"4.1.2-p1+galaxy1",
"4.1.1"
]
@@ -289777,6 +259533,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -289832,10 +259592,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -289878,11 +259634,6 @@
"state": "exact",
"version": "2.0.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -289927,6 +259678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -289984,10 +259739,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -290032,11 +259783,6 @@
"state": "exact",
"version": "2.30.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -290082,6 +259828,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -290135,10 +259885,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -290181,11 +259927,6 @@
"state": "exact",
"version": "2018.09.10+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2018.09.10+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -290241,7 +259982,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 84,
- "visitors": 7852,
+ "visitors": 7892,
"workflows": [
{
"creators": [
@@ -290298,7 +260039,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nRaw genome sequence\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Red\"];\n 0 -->|output| 1;\n 2[\"RepeatMasker\"];\n 0 -->|output| 2;\n 3d7a51a2-41f9-426f-b9e8-082fab12d6e2[\"Output\\nRepeatMasker repeat catalogue on input dataset(s)\"];\n 2 --> 3d7a51a2-41f9-426f-b9e8-082fab12d6e2;\n style 3d7a51a2-41f9-426f-b9e8-082fab12d6e2 stroke:#2c3143,stroke-width:4px;\n 3f0c419c-7bd2-4378-b174-fe11e52bbf61[\"Output\\nRepeatMasker masked sequence on input dataset(s)\"];\n 2 --> 3f0c419c-7bd2-4378-b174-fe11e52bbf61;\n style 3f0c419c-7bd2-4378-b174-fe11e52bbf61 stroke:#2c3143,stroke-width:4px;\n 342d5065-122b-437a-8f78-a636c5f2b7f6[\"Output\\nRepeatMasker output log on input dataset(s)\"];\n 2 --> 342d5065-122b-437a-8f78-a636c5f2b7f6;\n style 342d5065-122b-437a-8f78-a636c5f2b7f6 stroke:#2c3143,stroke-width:4px;\n 4a157f80-0d75-425b-858d-49c4a12f91a0[\"Output\\nRepeatMasker repeat statistics on input dataset(s)\"];\n 2 --> 4a157f80-0d75-425b-858d-49c4a12f91a0;\n style 4a157f80-0d75-425b-858d-49c4a12f91a0 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "RepeatMasker",
"outputs": [
{
@@ -290943,9 +260684,9 @@
"topic_4013"
],
"edam_operation": [
+ "Read mapping",
"Genome annotation",
- "Genome visualisation",
- "Read mapping"
+ "Genome visualisation"
],
"edam_topic": [
"Whole genome sequencing",
@@ -290958,8 +260699,7 @@
],
"exact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -291002,7 +260742,7 @@
"Get information about ARGs",
"Visualize the ARGs and plasmid genes in their genomic context"
],
- "pageviews": 2195,
+ "pageviews": 2256,
"pub_date": "2024-01-23",
"questions": [
"Which resistance genes are on a bacterial genome?",
@@ -291027,11 +260767,11 @@
"short_tools": [
"staramr_search",
"Grep1",
- "bakta",
- "bowtie2",
- "jbrowse",
"tbl2gff3",
- "upload1"
+ "upload1",
+ "jbrowse",
+ "bakta",
+ "bowtie2"
],
"slides": false,
"slides_recordings": false,
@@ -291047,11 +260787,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -291089,6 +260824,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -291144,10 +260883,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -291194,11 +260929,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -291243,6 +260973,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -291295,10 +261029,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -291339,10 +261069,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -291385,6 +261111,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -291409,9 +261139,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -291423,9 +261153,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -291449,10 +261179,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -291488,13 +261214,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -291508,17 +261234,12 @@
"state": "exact",
"version": "2.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.4.5+galaxy1",
"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -291565,6 +261286,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -291618,10 +261343,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -291664,11 +261385,6 @@
"state": "exact",
"version": "1.8.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -291718,6 +261434,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -291773,10 +261493,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -291812,23 +261528,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -291841,11 +261557,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -291891,6 +261602,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -291944,10 +261659,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -291990,11 +261701,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -292039,6 +261745,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -292073,10 +261783,10 @@
"state": "inexact",
"versions": [
"0.7.2+galaxy0",
+ "0.9.1+galaxy0",
"0.5.1",
- "0.2.1",
"0.8.0+galaxy0",
- "0.9.1+galaxy0"
+ "0.2.1"
]
},
{
@@ -292099,10 +261809,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -292148,11 +261854,6 @@
"state": "exact",
"version": "0.10.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.10.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -292202,6 +261903,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -292254,10 +261959,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -292298,10 +261999,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -292362,8 +262059,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 205,
- "visitors": 1603,
+ "visit_duration": 203,
+ "visitors": 1652,
"workflows": [
{
"creators": [
@@ -292385,7 +262082,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n 2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n 3[label=\"staramr\"]\n 0 -> 3 [label=\"output\"]\n k2f01e653531f44fe85a7b699a47ab683[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n 3 -> k2f01e653531f44fe85a7b699a47ab683\n 4[label=\"Bakta\"]\n 0 -> 4 [label=\"output\"]\n k4a680ee078c44733b9f0cb1a0ebcb174[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n 4 -> k4a680ee078c44733b9f0cb1a0ebcb174\n 5[label=\"Bowtie2\"]\n 1 -> 5 [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n ka3c861ca77bf41188f3ec452427aac79[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n 5 -> ka3c861ca77bf41188f3ec452427aac79\n 6[label=\"Select\"]\n 3 -> 6 [label=\"detailed_summary\"]\n 7[label=\"Table to GFF3\"]\n 6 -> 7 [label=\"out_file1\"]\n 8[label=\"JBrowse\"]\n 4 -> 8 [label=\"annotation_gff3\"]\n 7 -> 8 [label=\"output\"]\n 5 -> 8 [label=\"output\"]\n kcf90b47e652b428e817011929768a4d6[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n 8 -> kcf90b47e652b428e817011929768a4d6\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n 2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n 3[label=\"staramr\"]\n 0 -> 3 [label=\"output\"]\n k80c90033b1134ab0aa74bc854226af75[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n 3 -> k80c90033b1134ab0aa74bc854226af75\n 4[label=\"Bakta\"]\n 0 -> 4 [label=\"output\"]\n k136fe6f95bed4cfaa22693d7b18553a2[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n 4 -> k136fe6f95bed4cfaa22693d7b18553a2\n 5[label=\"Bowtie2\"]\n 1 -> 5 [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n kf33376aed46846b68c9f681067c2051e[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n 5 -> kf33376aed46846b68c9f681067c2051e\n 6[label=\"Select\"]\n 3 -> 6 [label=\"detailed_summary\"]\n 7[label=\"Table to GFF3\"]\n 6 -> 7 [label=\"out_file1\"]\n 8[label=\"JBrowse\"]\n 4 -> 8 [label=\"annotation_gff3\"]\n 7 -> 8 [label=\"output\"]\n 5 -> 8 [label=\"output\"]\n k20eae6766d394ec3a83dab27abd3ab91[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n 8 -> k20eae6766d394ec3a83dab27abd3ab91\n}",
"history": [
{
"hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
@@ -292500,8 +262197,8 @@
}
],
"license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"staramr\"];\n 0 -->|output| 3;\n 2f01e653-531f-44fe-85a7-b699a47ab683[\"Output\\nstararm_detailed_summary\"];\n 3 --> 2f01e653-531f-44fe-85a7-b699a47ab683;\n style 2f01e653-531f-44fe-85a7-b699a47ab683 stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174[\"Output\\nbakta_annotation_summary\"];\n 4 --> 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174;\n style 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174 stroke:#2c3143,stroke-width:4px;\n 5[\"Bowtie2\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n a3c861ca-77bf-4118-8f3e-c452427aac79[\"Output\\nbowtie_mapping_stats\"];\n 5 --> a3c861ca-77bf-4118-8f3e-c452427aac79;\n style a3c861ca-77bf-4118-8f3e-c452427aac79 stroke:#2c3143,stroke-width:4px;\n 6[\"Select\"];\n 3 -->|detailed_summary| 6;\n 7[\"Table to GFF3\"];\n 6 -->|out_file1| 7;\n 8[\"JBrowse\"];\n 4 -->|annotation_gff3| 8;\n 7 -->|output| 8;\n 5 -->|output| 8;\n cf90b47e-652b-428e-8170-11929768a4d6[\"Output\\njbrowse_output\"];\n 8 --> cf90b47e-652b-428e-8170-11929768a4d6;\n style cf90b47e-652b-428e-8170-11929768a4d6 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"staramr\"];\n 0 -->|output| 3;\n 80c90033-b113-4ab0-aa74-bc854226af75[\"Output\\nstararm_detailed_summary\"];\n 3 --> 80c90033-b113-4ab0-aa74-bc854226af75;\n style 80c90033-b113-4ab0-aa74-bc854226af75 stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n 136fe6f9-5bed-4cfa-a226-93d7b18553a2[\"Output\\nbakta_annotation_summary\"];\n 4 --> 136fe6f9-5bed-4cfa-a226-93d7b18553a2;\n style 136fe6f9-5bed-4cfa-a226-93d7b18553a2 stroke:#2c3143,stroke-width:4px;\n 5[\"Bowtie2\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n f33376ae-d468-46b6-8c9f-681067c2051e[\"Output\\nbowtie_mapping_stats\"];\n 5 --> f33376ae-d468-46b6-8c9f-681067c2051e;\n style f33376ae-d468-46b6-8c9f-681067c2051e stroke:#2c3143,stroke-width:4px;\n 6[\"Select\"];\n 3 -->|detailed_summary| 6;\n 7[\"Table to GFF3\"];\n 6 -->|out_file1| 7;\n 8[\"JBrowse\"];\n 4 -->|annotation_gff3| 8;\n 7 -->|output| 8;\n 5 -->|output| 8;\n 20eae676-6d39-4ec3-a83d-ab27abd3ab91[\"Output\\njbrowse_output\"];\n 8 --> 20eae676-6d39-4ec3-a83d-ab27abd3ab91;\n style 20eae676-6d39-4ec3-a83d-ab27abd3ab91 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "mrsa AMR gene detection",
"outputs": [
{
@@ -292573,7 +262270,7 @@
{
"label": "stararm_detailed_summary",
"output_name": "detailed_summary",
- "uuid": "2f01e653-531f-44fe-85a7-b699a47ab683"
+ "uuid": "80c90033-b113-4ab0-aa74-bc854226af75"
}
]
},
@@ -292647,7 +262344,7 @@
{
"label": "bakta_annotation_summary",
"output_name": "annotation_tsv",
- "uuid": "4a680ee0-78c4-4733-b9f0-cb1a0ebcb174"
+ "uuid": "136fe6f9-5bed-4cfa-a226-93d7b18553a2"
}
]
},
@@ -292704,7 +262401,7 @@
{
"label": "bowtie_mapping_stats",
"output_name": "mapping_stats",
- "uuid": "a3c861ca-77bf-4118-8f3e-c452427aac79"
+ "uuid": "f33376ae-d468-46b6-8c9f-681067c2051e"
}
]
},
@@ -292757,7 +262454,7 @@
{
"label": "jbrowse_output",
"output_name": "output",
- "uuid": "cf90b47e-652b-428e-8170-11929768a4d6"
+ "uuid": "20eae676-6d39-4ec3-a83d-ab27abd3ab91"
}
]
}
@@ -292831,114 +262528,7 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n owner: devteam\n revisions: d6694932c5e0\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n owner: iuc\n revisions: e483be1014b6\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n owner: iuc\n revisions: 5efbd15675ca\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
- "contributions": {
- "authorship": [
- "estebanpw"
- ],
- "reviewing": [
- "shiltemann",
- "deeptivarshney",
- "hexylena",
- "gallardoalba",
- "estebanpw"
- ]
- },
"contributors": [
- {
- "elixir_node": "es",
- "email": "estebanpw@uma.es",
- "id": "estebanpw",
- "joined": "2020-11",
- "name": "Esteban Perez-Wohlfeil",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "deeptivarshney",
- "joined": "2022-12",
- "name": "Deepti Varshney",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
{
"elixir_node": "es",
"email": "estebanpw@uma.es",
@@ -292984,7 +262574,7 @@
"Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
"Learn how to post-process your sequence comparisons"
],
- "pageviews": 6017727,
+ "pageviews": 6040710,
"pub_date": "2021-02-08",
"questions": [
"How can we run pairwise genome comparisons using Galaxy?",
@@ -293002,10 +262592,10 @@
],
"short_id": "T00176",
"short_tools": [
- "tp_awk_tool",
- "clustalw",
"chromeister",
- "gecko"
+ "gecko",
+ "clustalw",
+ "tp_awk_tool"
],
"slides": true,
"slides_recordings": false,
@@ -293062,6 +262652,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -293117,10 +262711,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -293167,11 +262757,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -293216,6 +262801,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -293270,10 +262859,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -293320,11 +262905,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -293370,6 +262950,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -293424,10 +263008,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -293473,11 +263053,6 @@
"state": "exact",
"version": "2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -293523,6 +263098,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -293578,10 +263157,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -293627,13 +263202,6 @@
"state": "exact",
"version": "1.5.a"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.5.a+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -293677,6 +263245,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -293730,10 +263302,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -293777,10 +263345,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -293836,7 +263400,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 286,
- "visitors": 2197065,
+ "visitors": 2207898,
"workflows": [
{
"creators": [],
@@ -293937,7 +263501,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Chromeister\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n 2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n 2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n 2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n 5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n 2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n 2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n 9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n 2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "CHROMEISTER chromosome comparison",
"outputs": [
{
@@ -294253,7 +263817,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Gecko\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n 2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n 3[\"Text reformatting\"];\n 2 -->|alignments2| 3;\n 4[\"ClustalW\"];\n 3 -->|outfile| 4;\n d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n 4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n 4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GECKO pairwise comparison",
"outputs": [
{
@@ -294833,14 +264397,14 @@
],
"edam_operation": [
"Genome assembly",
- "Sequence annotation",
- "Sequence assembly validation",
"Genome annotation",
- "Gene prediction",
- "Differential protein expression profiling",
- "Genome visualisation",
+ "Sequence assembly validation",
+ "Sequence annotation",
+ "Transcriptome assembly",
"Scaffolding",
- "Transcriptome assembly"
+ "Differential protein expression profiling",
+ "Gene prediction",
+ "Genome visualisation"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -294867,7 +264431,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 362,
+ "pageviews": 394,
"pub_date": "2024-08-21",
"questions": [
"How to annotate an eukaryotic genome with Helixer?",
@@ -294884,12 +264448,12 @@
],
"short_id": "T00451",
"short_tools": [
- "gffread",
- "jbrowse",
- "omark",
"jcvi_gff_stats",
"helixer",
- "busco"
+ "gffread",
+ "jbrowse",
+ "busco",
+ "omark"
],
"slides": false,
"slides_recordings": false,
@@ -294920,6 +264484,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -294975,10 +264543,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -295025,11 +264589,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -295074,6 +264633,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295129,10 +264692,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -295166,10 +264725,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -295184,11 +264743,6 @@
"state": "exact",
"version": "2.2.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -295238,6 +264792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295290,10 +264848,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -295338,11 +264892,6 @@
"state": "exact",
"version": "0.3.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -295389,6 +264938,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295421,10 +264974,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -295447,10 +265000,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -295498,23 +265047,18 @@
"state": "exact",
"version": "5.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -295557,6 +265101,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295589,10 +265137,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -295615,10 +265163,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -295666,23 +265210,18 @@
"state": "exact",
"version": "5.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -295725,6 +265264,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295780,10 +265323,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -295819,23 +265358,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -295848,11 +265387,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -295898,6 +265432,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -295950,10 +265488,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -295997,11 +265531,6 @@
"state": "exact",
"version": "0.8.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -296047,6 +265576,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -296099,10 +265632,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -296144,11 +265673,6 @@
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- "state": "exact",
- "version": "0.3.0+galaxy2"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -296192,6 +265716,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -296244,10 +265772,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -296288,10 +265812,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -296350,8 +265870,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 95,
- "visitors": 307,
+ "visit_duration": 99,
+ "visitors": 328,
"workflows": [
{
"creators": [
@@ -296446,7 +265966,7 @@
],
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- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "annotation_helixer",
"outputs": [
{
@@ -297008,62 +266528,7 @@
},
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- "reviewing": [
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- "paulzierep"
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- "elixir-europe"
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- "id": "paulzierep",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
{
"affiliations": [
"uni-freiburg",
@@ -297081,11 +266546,11 @@
"dir": "topics/genome-annotation/tutorials/secondary-metabolite-discovery",
"draft": true,
"edam_operation": [
- "Sequence clustering",
"Data handling",
"Gene prediction",
+ "Differential gene expression analysis",
"Service invocation",
- "Differential gene expression analysis"
+ "Sequence clustering"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -297113,7 +266578,7 @@
"Extraction of gene cluster products using a custom script.",
"Query of the products in compound libraries using cheminformatic tools."
],
- "pageviews": 368,
+ "pageviews": 404,
"pub_date": "2024-02-21",
"questions": [
"How to discover secondary metabolites produced by microorganisms ?",
@@ -297122,19 +266587,19 @@
],
"short_id": "T00420",
"short_tools": [
- "ctb_silicos_qed",
- "ctb_simsearch",
- "antismash",
- "tp_awk_tool",
+ "collapse_dataset",
"bp_genbank2gff3",
"ctb_np-likeness-calculator",
- "ncbi_acc_download",
+ "tp_awk_tool",
"Remove beginning1",
- "ctb_chemfp_mol2fps",
+ "ncbi_acc_download",
"edu.tamu.cpt.gff3.customGbkToGff",
- "interactive_tool_jupyter_notebook",
+ "antismash",
+ "ctb_silicos_qed",
+ "ctb_chemfp_mol2fps",
"openbabel_remDuplicates",
- "collapse_dataset"
+ "interactive_tool_jupyter_notebook",
+ "ctb_simsearch"
],
"slides": false,
"slides_recordings": false,
@@ -297170,6 +266635,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -297225,10 +266694,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -297275,11 +266740,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -297324,6 +266784,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -297376,10 +266840,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -297420,10 +266880,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -297466,6 +266922,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -297518,10 +266978,6 @@
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"state": "missing"
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{
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"state": "missing"
@@ -297562,10 +267018,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
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{
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"state": "missing"
@@ -297608,6 +267060,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -297661,10 +267117,6 @@
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@@ -297707,10 +267159,6 @@
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{
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"state": "exact",
@@ -297756,6 +267204,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -297808,10 +267260,6 @@
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@@ -297857,10 +267305,6 @@
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"state": "exact",
@@ -299210,11 +268619,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -299279,8 +268683,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 60,
- "visitors": 281,
+ "visit_duration": 63,
+ "visitors": 300,
"workflows": [
{
"creators": [],
@@ -299386,7 +268790,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"NCBI Accession Download\"];\n 0 -->|output| 3;\n faecdec3-711d-43ba-bb91-38a4b4b3932d[\"Output\\nNCBI Accession Download on input dataset(s): Log\"];\n 3 --> faecdec3-711d-43ba-bb91-38a4b4b3932d;\n style faecdec3-711d-43ba-bb91-38a4b4b3932d stroke:#2c3143,stroke-width:4px;\n c8857c6f-ec99-4d29-8c98-be7a63a9f029[\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"];\n 3 --> c8857c6f-ec99-4d29-8c98-be7a63a9f029;\n style c8857c6f-ec99-4d29-8c98-be7a63a9f029 stroke:#2c3143,stroke-width:4px;\n 4[\"Molecule to fingerprint\"];\n 2 -->|output| 4;\n 5[\"Antismash\"];\n 3 -->|output| 5;\n cc813ad7-f423-4cb8-ba79-8201abab206a[\"Output\\nAntismash on input dataset(s): HTML report\"];\n 5 --> cc813ad7-f423-4cb8-ba79-8201abab206a;\n style cc813ad7-f423-4cb8-ba79-8201abab206a stroke:#2c3143,stroke-width:4px;\n 6[\"Collapse clusters in one Genbank entry\"];\n 5 -->|genbank| 6;\n 7[\"Extract SMILES qualifiers\"];\n 1 -->|output| 7;\n 6 -->|output| 7;\n 8[\"Convert table to smi format\"];\n 7 -->|output_collection| 8;\n 9[\"Remove beginning\"];\n 8 -->|outfile| 9;\n 10[\"Remove duplicated molecules\"];\n 9 -->|out_file1| 10;\n 11[\"Molecule to fingerprint\"];\n 10 -->|outfile| 11;\n 12[\"Natural Product\"];\n 10 -->|outfile| 12;\n 13[\"Drug-likeness\"];\n 10 -->|outfile| 13;\n 14[\"Similarity Search\"];\n 11 -->|outfile| 14;\n 4 -->|outfile| 14;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Gene Cluster Product Similarity Search ",
"outputs": [
{
@@ -299998,15 +269402,15 @@
"topic_0798"
],
"edam_operation": [
- "Sequence motif recognition",
- "Nucleic acid feature detection",
"Structural variation detection",
+ "Protein feature detection",
"Genome assembly",
"Genome annotation",
- "Protein feature detection",
- "Genome visualisation",
+ "Sequence motif recognition",
"Scaffolding",
- "Multilocus sequence typing"
+ "Nucleic acid feature detection",
+ "Multilocus sequence typing",
+ "Genome visualisation"
],
"edam_topic": [
"Genomics",
@@ -300018,8 +269422,7 @@
"Mobile genetic elements"
],
"exact_supported_servers": [
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -300072,7 +269475,7 @@
"Process the outputs to formate them for visualization needs",
"Visualize a draft bacterial genome and its annotations"
],
- "pageviews": 4233,
+ "pageviews": 4366,
"pub_date": "2024-02-01",
"questions": [
"Which genes are on a draft bacterial genome?",
@@ -300095,16 +269498,16 @@
],
"short_id": "T00403",
"short_tools": [
- "bakta",
"tp_replace_in_column",
+ "plasmidfinder",
+ "tp_tail_tool",
+ "Grouping1",
"isescan",
- "jbrowse",
"tbl2gff3",
- "plasmidfinder",
"integron_finder",
"upload1",
- "Grouping1",
- "tp_tail_tool"
+ "jbrowse",
+ "bakta"
],
"slides": false,
"slides_recordings": false,
@@ -300115,11 +269518,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -300162,6 +269560,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -300217,10 +269619,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -300267,11 +269665,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -300316,6 +269709,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -300368,10 +269765,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -300412,10 +269805,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -300458,6 +269847,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -300516,10 +269909,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -300573,11 +269962,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -300628,6 +270012,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -300686,10 +270074,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -300739,11 +270123,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -300791,6 +270170,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -300816,8 +270199,8 @@
"state": "inexact",
"versions": [
"1.8.1+galaxy1",
- "1.9.2+galaxy0",
- "1.8.2+galaxy0"
+ "1.8.2+galaxy0",
+ "1.9.2+galaxy0"
]
},
{
@@ -300848,10 +270231,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -300897,11 +270276,6 @@
"state": "exact",
"version": "1.9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -300920,10 +270294,10 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.2+galaxy0",
"1.8.2+galaxy0",
- "1.9.4+galaxy0",
- "1.5.0+galaxy0"
+ "1.9.2+galaxy0",
+ "1.5.0+galaxy0",
+ "1.9.4+galaxy0"
]
},
{
@@ -300956,6 +270330,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -301014,10 +270392,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -301062,11 +270436,6 @@
"state": "exact",
"version": "2.0.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -301111,6 +270480,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -301169,10 +270542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -301217,11 +270586,6 @@
"state": "exact",
"version": "1.7.2.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7.2.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -301266,6 +270630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -301321,10 +270689,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -301360,23 +270724,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -301389,11 +270753,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -301439,6 +270798,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -301492,10 +270855,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -301538,11 +270897,6 @@
"state": "exact",
"version": "2.1.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.6+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -301587,6 +270941,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -301640,10 +270998,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -301686,11 +271040,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -301735,6 +271084,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -301787,10 +271140,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -301831,10 +271180,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -301897,8 +271242,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 162,
- "visitors": 3101,
+ "visit_duration": 163,
+ "visitors": 3187,
"workflows": [
{
"creators": [
@@ -301968,7 +271313,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"ISEScan\"];\n 0 -->|output| 1;\n 2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n 1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n 2[\"PlasmidFinder\"];\n 0 -->|output| 2;\n 614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n 2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n 3[\"Integron Finder\"];\n 0 -->|output| 3;\n d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n 3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n 4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n 5[\"Group\"];\n 1 -->|all_results| 5;\n 6[\"Group\"];\n 1 -->|all_results| 6;\n 7[\"Replace Text\"];\n 2 -->|result_file| 7;\n 8[\"Select last\"];\n 7 -->|outfile| 8;\n 9[\"Table to GFF3\"];\n 8 -->|outfile| 9;\n 10[\"JBrowse\"];\n 0 -->|output| 10;\n 4 -->|annotation_gff3| 10;\n 9 -->|output| 10;\n 1 -->|annotation| 10;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Bacterial Genome Annotation",
"outputs": [
{
@@ -302254,23 +271599,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/tutorial.json",
- "contributions": {
- "authorship": [
- "abretaud",
- "hexylena"
- ],
- "reviewing": [
- "hexylena",
- "bgruening",
- "bebatut",
- "abretaud",
- "rlibouba",
- "shiltemann",
- "gallardoalba",
- "stephanierobin",
- "simonbray"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -302325,199 +271653,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
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- "state": "local"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "local"
- }
- ],
- "version": "local"
- },
- {
- "id": "cat1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "local"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -304264,10 +272968,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -304308,10 +273008,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -304332,7 +273028,7 @@
"version": "local"
},
{
- "id": "join1",
+ "id": "Filter1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -304354,6 +273050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -304364,7 +273064,7 @@
},
{
"server": "http://dintor.eurac.edu/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://www.freebioinfo.org/",
@@ -304407,9 +273107,143 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "cat1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
"state": "local"
},
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -304451,7 +273285,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "join1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -304496,6 +273464,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -304555,10 +273527,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -304601,11 +273569,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -304651,6 +273614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -304709,10 +273676,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -304755,11 +273718,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -304805,6 +273763,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -304863,10 +273825,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -304909,11 +273867,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -304959,6 +273912,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305014,10 +273971,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -305060,11 +274013,6 @@
"state": "exact",
"version": "0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -305112,6 +274060,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305169,10 +274121,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -305208,9 +274156,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -305218,8 +274166,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -305228,11 +274176,6 @@
"state": "exact",
"version": "1.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -305278,6 +274221,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305338,10 +274285,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -305375,9 +274318,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -305391,11 +274334,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -305441,6 +274379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305493,10 +274435,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -305541,11 +274479,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -305591,6 +274524,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305645,10 +274582,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -305693,11 +274626,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -305743,6 +274671,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305799,10 +274731,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -305851,11 +274779,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -305903,6 +274826,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -305955,10 +274882,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -306003,10 +274926,6 @@
"state": "exact",
"version": "0.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -306050,6 +274969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -306103,10 +275026,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -306149,11 +275068,6 @@
"state": "exact",
"version": "2.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.3.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -306198,6 +275112,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -306252,10 +275170,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -306303,11 +275217,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -306353,6 +275262,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -306389,8 +275302,8 @@
"state": "inexact",
"versions": [
"7.221.3",
- "7.508+galaxy0",
- "7.475+galaxy0"
+ "7.475+galaxy0",
+ "7.508+galaxy0"
]
},
{
@@ -306413,10 +275326,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -306466,11 +275375,6 @@
"state": "exact",
"version": "7.489+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "7.489+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -306545,8 +275449,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 198,
- "visitors": 1163,
+ "visit_duration": 197,
+ "visitors": 1172,
"workflows": [
{
"creators": [
@@ -306655,7 +275559,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nDiamond makedb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nORFipy BED\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Diamond: Find hits in ORFs\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Column Regex Find And Replace\"];\n 2 -->|output| 4;\n 5[\"Alignments\"];\n 3 -->|daa_output| 5;\n 6[\"Cut\"];\n 4 -->|out_file1| 6;\n 7[\"Alignments + BED\"];\n 6 -->|out_file1| 7;\n 5 -->|blast_tabular| 7;\n 8[\"Cut\"];\n 7 -->|out_file1| 8;\n 9[\"Collapse Collection\"];\n 7 -->|out_file1| 9;\n 10[\"Intersect\"];\n 6 -->|out_file1| 10;\n 8 -->|out_file1| 10;\n 11[\"Filter\"];\n 9 -->|output| 11;\n 12[\"Overlapping ORFs\"];\n 10 -->|output| 12;\n 13[\"Cut\"];\n 11 -->|out_file1| 13;\n 14[\"Compute\"];\n 12 -->|output| 14;\n 15[\"Compute\"];\n 13 -->|out_file1| 15;\n 16[\"Split file\"];\n 15 -->|out_file1| 16;\n 17[\"Report\"];\n 15 -->|out_file1| 17;\n 18[\"Tabular-to-FASTA\"];\n 16 -->|split_output| 18;\n 19[\"Cut\"];\n 17 -->|out_file1| 19;\n 20[\"MAFFT\"];\n 18 -->|output| 20;\n 21[\"Filter: Plus strand matches\"];\n 19 -->|out_file1| 21;\n 22[\"Filter: Minus strand matches\"];\n 19 -->|out_file1| 22;\n 23[\"Join neighbors\"];\n 20 -->|outputAlignment| 23;\n 54ea37cc-63d1-422a-9f5e-124b8d39e6bd[\"Output\\nJoin neighbors on input dataset(s): Calculated distances\"];\n 23 --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;\n style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd stroke:#2c3143,stroke-width:4px;\n 24[\"Compute\"];\n 21 -->|out_file1| 24;\n 25[\"Compute\"];\n 22 -->|out_file1| 25;\n 26[\"Concatenate datasets\"];\n 24 -->|out_file1| 26;\n 25 -->|out_file1| 26;\n 27[\"Compute\"];\n 26 -->|out_file1| 27;\n 28[\"Cut\"];\n 27 -->|out_file1| 28;\n 29[\"Compute\"];\n 28 -->|out_file1| 29;\n 30[\"Join two Datasets\"];\n 14 -->|out_file1| 30;\n 29 -->|out_file1| 30;\n 31[\"Mapping report\"];\n 30 -->|out_file1| 31;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Comparative gene analysis",
"outputs": [
{
@@ -307348,26 +276252,25 @@
],
"dir": "topics/genome-annotation/tutorials/funannotate",
"edam_operation": [
- "Sequence motif recognition",
- "Genome visualisation",
- "Formatting",
- "Genome assembly",
- "Sequence annotation",
"Fold recognition",
- "Information extraction",
- "Sequence alignment",
- "Sequence assembly validation",
"Homology-based gene prediction",
+ "Information extraction",
+ "Genome assembly",
"Genome annotation",
+ "Sequence assembly validation",
+ "Sequence annotation",
+ "Sequence motif recognition",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Formatting",
"Protein feature detection",
"Query and retrieval",
- "Transcriptome assembly",
- "Scaffolding"
+ "Sequence alignment",
+ "Genome visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -307409,7 +276312,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 11690,
+ "pageviews": 11741,
"priority": 2,
"pub_date": "2021-11-29",
"questions": [
@@ -307455,15 +276358,15 @@
],
"short_id": "T00172",
"short_tools": [
- "eggnog_mapper",
- "picard_MergeSamFiles",
- "busco",
- "jbrowse",
"funannotate_predict",
- "interproscan",
- "funannotate_compare",
"funannotate_annotate",
+ "jbrowse",
+ "busco",
"rna_star",
+ "funannotate_compare",
+ "interproscan",
+ "eggnog_mapper",
+ "picard_MergeSamFiles",
"aegean_parseval"
],
"slides": false,
@@ -307476,11 +276379,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -307527,6 +276425,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -307582,10 +276484,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -307632,11 +276530,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -307681,6 +276574,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -307733,10 +276630,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -307769,8 +276662,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "5.52-86.0+galaxy1",
- "5.54-87.0+galaxy2"
+ "5.54-87.0+galaxy2",
+ "5.52-86.0+galaxy1"
]
},
{
@@ -307783,11 +276676,6 @@
"state": "exact",
"version": "5.59-91.0+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.59-91.0+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -307833,6 +276721,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -307887,10 +276779,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -307937,11 +276825,6 @@
"state": "exact",
"version": "2.18.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -307987,6 +276870,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308039,10 +276926,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308092,11 +276975,6 @@
"state": "exact",
"version": "2.1.8+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.8+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -308145,6 +277023,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308197,10 +277079,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308244,11 +277122,6 @@
"state": "exact",
"version": "0.16.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.16.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -308293,6 +277166,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308346,10 +277223,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308395,23 +277268,18 @@
"state": "exact",
"version": "5.4.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.4.6+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -308454,6 +277322,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308506,10 +277378,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308557,11 +277425,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -308577,10 +277440,10 @@
"versions": [
"1.8.9+galaxy2",
"1.8.15+galaxy5",
- "1.8.15+galaxy3",
- "1.8.15+galaxy1",
- "1.8.15+galaxy4",
"1.8.9+galaxy3",
+ "1.8.15+galaxy4",
+ "1.8.15+galaxy1",
+ "1.8.15+galaxy3",
"1.8.15+galaxy2"
]
},
@@ -308614,6 +277477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308666,10 +277533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308717,11 +277580,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -308766,6 +277624,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308818,10 +277680,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -308869,11 +277727,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -308890,10 +277743,10 @@
"1.8.9+galaxy2",
"1.8.15+galaxy5",
"1.8.15+galaxy1",
- "1.8.15+galaxy4",
"1.8.15+galaxy2",
"1.8.9+galaxy3",
- "1.8.15+galaxy3"
+ "1.8.15+galaxy3",
+ "1.8.15+galaxy4"
]
},
{
@@ -308926,6 +277779,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -308978,10 +277835,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -309029,11 +277882,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -309078,6 +277926,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -309130,10 +277982,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -309182,11 +278030,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -309202,11 +278045,11 @@
"versions": [
"1.8.15+galaxy5",
"1.8.9+galaxy2",
- "1.8.9+galaxy3",
- "1.8.15+galaxy2",
- "1.8.15+galaxy1",
+ "1.8.15+galaxy3",
"1.8.15+galaxy4",
- "1.8.15+galaxy3"
+ "1.8.15+galaxy1",
+ "1.8.15+galaxy2",
+ "1.8.9+galaxy3"
]
},
{
@@ -309239,6 +278082,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -309291,10 +278138,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -309343,11 +278186,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -309392,6 +278230,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -309447,10 +278289,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -309486,23 +278324,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -309515,11 +278353,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -309565,6 +278398,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -309590,8 +278427,8 @@
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -309628,10 +278465,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -309670,16 +278503,16 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
@@ -309692,11 +278525,6 @@
"state": "exact",
"version": "2.7.10b+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.10b+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -309749,6 +278577,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -309808,10 +278640,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -309850,24 +278678,24 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -309875,11 +278703,6 @@
"state": "exact",
"version": "2.7.8a+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.8a+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -309948,7 +278771,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 125,
- "visitors": 7847,
+ "visitors": 7893,
"workflows": [
{
"creators": [
@@ -310161,7 +278984,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"RNA STAR\"];\n 0 -->|output| 7;\n 1 -->|output| 7;\n 2 -->|output| 7;\n 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n 7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n 8[\"Funannotate predict annotation\"];\n 3 -->|output| 8;\n 7 -->|mapped_reads| 8;\n 0 -->|output| 8;\n 9[\"eggNOG Mapper\"];\n 8 -->|fasta_proteins| 9;\n 10[\"InterProScan\"];\n 8 -->|fasta_proteins| 10;\n 11[\"Funannotate functional\"];\n 9 -->|annotations| 11;\n 8 -->|annot_gbk| 11;\n 10 -->|outfile_xml| 11;\n 4 -->|output| 11;\n d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n 11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n 9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n 11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n 99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n 11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n 17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n 11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n 4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n 11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n 12[\"JBrowse\"];\n 0 -->|output| 12;\n 11 -->|gff3| 12;\n 7 -->|mapped_reads| 12;\n ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n 12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n 13[\"Funannotate compare\"];\n 5 -->|output| 13;\n 11 -->|gbk| 13;\n e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n 13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n 14[\"AEGeAn ParsEval\"];\n 6 -->|output| 14;\n 11 -->|gff3| 14;\n 0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n 14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n 15[\"Busco\"];\n 11 -->|fa_proteins| 15;\n 57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n 15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n 97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n 15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Funannotate",
"outputs": [
{
@@ -311103,17 +279926,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n owner: devteam\n revisions: 0232f19d300f\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 1440ae06552f\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions: 2bb2e07a7a21\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n owner: iuc\n revisions: 8cffbd184762\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n owner: iuc\n revisions: 96ac930d84fa\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n owner: iuc\n revisions: 326f9c294b09\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n owner: simon-gladman\n revisions: 20ca2574216a\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
- "contributions": {
- "authorship": [
- "abretaud"
- ],
- "reviewing": [
- "bgruening",
- "bebatut",
- "abretaud",
- "hexylena"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -311139,128 +279951,17 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
"twitter": "abretau",
"url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
"edam_operation": [
+ "Transcriptome assembly",
+ "Genome assembly",
"Genome annotation",
"Sequence assembly validation",
- "Genome assembly",
"Sequence annotation",
"Genome visualisation",
- "Scaffolding",
- "Transcriptome assembly"
+ "Scaffolding"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -311289,7 +279990,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 4428,
+ "pageviews": 4550,
"priority": 3,
"pub_date": "2021-01-12",
"questions": [
@@ -311298,13 +279999,13 @@
],
"short_id": "T00167",
"short_tools": [
+ "maker",
+ "jcvi_gff_stats",
+ "maker_map_ids",
"fasta-stats",
"gffread",
"jbrowse",
- "jcvi_gff_stats",
- "maker_map_ids",
- "busco",
- "maker"
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -311341,6 +280042,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -311396,10 +280101,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -311446,11 +280147,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -311495,6 +280191,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -311550,10 +280250,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -311599,14 +280295,6 @@
"state": "exact",
"version": "2.2.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1.3+galaxy0",
- "2.2.1.4+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -311621,8 +280309,8 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
"2.2.1.2",
+ "2.2.1.0",
"2.2.1.3+galaxy0",
"2.2.1.4+galaxy0"
]
@@ -311666,6 +280354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -311698,10 +280390,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -311724,10 +280416,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -311775,53 +280463,36 @@
"state": "exact",
"version": "3.0.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
- "5.2.2+galaxy2",
- "5.3.1+galaxy0",
- "5.3.2+galaxy0",
- "5.5.0+galaxy0",
- "5.2.2+galaxy0",
- "5.7.1+galaxy0",
- "5.8.0+galaxy0",
- "5.4.5+galaxy0",
- "5.2.2+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "5.4.6+galaxy0",
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
+ "5.4.6+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "3.0.2+galaxy2",
- "4.1.2",
"5.3.2+galaxy0",
"5.5.0+galaxy0",
- "5.2.2+galaxy0",
+ "3.0.2+galaxy2",
+ "5.8.0+galaxy0",
"5.7.1+galaxy0",
- "5.8.0+galaxy0"
+ "4.1.2",
+ "5.2.2+galaxy0"
]
},
{
@@ -311859,6 +280530,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -311922,10 +280597,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -311974,17 +280645,6 @@
"state": "exact",
"version": "1.16.4+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.16.9+galaxy0",
- "1.16.11+galaxy1",
- "1.16.10+galaxy0",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -312034,6 +280694,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -312086,10 +280750,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -312133,11 +280793,6 @@
"state": "exact",
"version": "0.8.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -312183,6 +280838,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -312215,8 +280874,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.31.11",
- "2.31.10+galaxy1"
+ "2.31.10+galaxy1",
+ "2.31.11"
]
},
{
@@ -312239,10 +280898,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -312291,20 +280946,12 @@
"state": "exact",
"version": "2.31.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11+galaxy1",
- "2.31.11+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.31.11",
"2.31.10+galaxy1",
+ "2.31.11",
"2.31.11+galaxy1",
"2.31.11+galaxy2"
]
@@ -312313,8 +280960,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "2.31.11",
"2.31.10+galaxy1",
+ "2.31.11",
"2.31.11+galaxy1",
"2.31.11+galaxy2"
]
@@ -312358,6 +281005,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -312410,10 +281061,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -312461,13 +281108,6 @@
"state": "exact",
"version": "2.31.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -312513,6 +281153,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -312566,10 +281210,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -312611,10 +281251,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -312673,8 +281309,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 194,
- "visitors": 3050,
+ "visit_duration": 192,
+ "visitors": 3138,
"workflows": [
{
"creators": [],
@@ -312896,7 +281532,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Fasta Statistics\"];\n 0 -->|output| 5;\n 6[\"Busco\"];\n 0 -->|output| 6;\n 7[\"Maker\"];\n 4 -->|output| 7;\n 3 -->|output| 7;\n 1 -->|output| 7;\n 0 -->|output| 7;\n 2 -->|output| 7;\n 8[\"Map annotation ids\"];\n 7 -->|output_gff| 8;\n 9[\"Genome annotation statistics\"];\n 8 -->|renamed| 9;\n 0 -->|output| 9;\n 10[\"gffread\"];\n 8 -->|renamed| 10;\n 0 -->|output| 10;\n 11[\"JBrowse\"];\n 0 -->|output| 11;\n 8 -->|renamed| 11;\n 7 -->|output_evidences| 11;\n 12[\"Busco\"];\n 10 -->|output_exons| 12;\n 6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n 12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome annotation with Maker (short)",
"outputs": [
{
@@ -313651,19 +282287,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_coverage\n owner: bgruening\n revisions: bb1e4f63e0e6\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: find_subsequences\n owner: bgruening\n revisions: d882a0a75759\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie_wrappers\n owner: devteam\n revisions: b46e7d48076a\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n owner: devteam\n revisions: be25c075ed54\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gff_to_prot\n owner: iuc\n revisions: 07d7991bf205\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: transit_gumbel\n owner: iuc\n revisions: f50807720df1\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 49370cb85f0f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json",
- "contributions": {
- "authorship": [
- "delphine-l",
- "bebatut"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening",
- "hexylena",
- "bebatut",
- "delphine-l"
- ]
- },
"contributors": [
{
"email": "delphine.lariviere@galaxy.org",
@@ -313699,134 +282322,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
"twitter": "bebatut",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "delphine.lariviere@galaxy.org",
- "id": "delphine-l",
- "joined": "2017-09",
- "name": "Delphine Lariviere",
- "orcid": "0000-0001-6421-3484",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
}
],
"dir": "topics/genome-annotation/tutorials/tnseq",
@@ -313838,9 +282333,9 @@
],
"edam_operation": [
"Transposon prediction",
+ "Primer removal",
"Read pre-processing",
- "Sequence trimming",
- "Primer removal"
+ "Sequence trimming"
],
"edam_topic": [
"Genomics",
@@ -313879,7 +282374,7 @@
"Predict Essential genes with Transit",
"Compare gene essentiality in control sample and an different experimental condition"
],
- "pageviews": 6192308,
+ "pageviews": 6215319,
"priority": 4,
"pub_date": "2019-07-02",
"questions": [
@@ -313889,18 +282384,18 @@
],
"short_id": "T00179",
"short_tools": [
- "tp_easyjoin_tool",
- "gff_to_prot",
- "bg_find_subsequences",
- "cutadapt",
- "deeptools_bam_coverage",
- "Filter1",
- "__EXTRACT_DATASET__",
"tp_sort_header_tool",
- "Add_a_column1",
+ "Filter1",
"Cut1",
"transit_gumbel",
- "bowtie_wrapper"
+ "bg_find_subsequences",
+ "Add_a_column1",
+ "tp_easyjoin_tool",
+ "cutadapt",
+ "__EXTRACT_DATASET__",
+ "bowtie_wrapper",
+ "gff_to_prot",
+ "deeptools_bam_coverage"
],
"slides": true,
"slides_recordings": false,
@@ -313958,6 +282453,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -314013,10 +282512,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -314063,11 +282558,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -314112,6 +282602,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -314164,10 +282658,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -314208,10 +282698,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -314254,6 +282740,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -314306,10 +282796,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -314350,10 +282836,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -314396,6 +282878,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -314448,10 +282934,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -314492,10 +282974,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -314538,6 +283016,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -314562,9 +283044,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "3.1.2.0.0",
+ "3.3.0.0.0",
"3.5.1.0.0",
- "3.3.0.0.0"
+ "3.1.2.0.0"
]
},
{
@@ -314598,10 +283080,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -314651,11 +283129,6 @@
"state": "exact",
"version": "3.3.2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.2.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -314701,6 +283174,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -314753,10 +283230,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -314800,10 +283273,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -314849,6 +283318,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -314903,10 +283376,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -314953,11 +283422,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315003,6 +283467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315057,10 +283525,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
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@@ -315107,11 +283571,6 @@
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315157,6 +283616,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315209,10 +283672,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -315257,10 +283716,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315305,6 +283760,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315365,10 +283824,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -315409,8 +283864,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -315419,11 +283874,6 @@
"state": "exact",
"version": "1.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315469,6 +283919,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315521,10 +283975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -315568,10 +284018,6 @@
"state": "exact",
"version": "3.0.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315617,6 +284063,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315669,10 +284119,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -315718,10 +284164,6 @@
"state": "exact",
"version": "3.0.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -315767,6 +284209,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -315806,8 +284252,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -315830,10 +284276,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -315891,47 +284333,22 @@
"4.7+galaxy0",
"4.4+galaxy0",
"1.16.3",
- "1.6",
"1.16.1",
- "3.5+galaxy0",
+ "1.6",
+ "4.0+galaxy1",
"3.4+galaxy2",
- "4.6+galaxy0",
- "1.16",
+ "1.1.a",
+ "3.7+galaxy0",
+ "3.5+galaxy2",
"3.4+galaxy1",
"4.6+galaxy1",
"3.4+galaxy0",
- "3.7+galaxy0",
- "1.1.a",
- "4.8+galaxy0",
+ "1.16",
"4.9+galaxy0",
- "4.0+galaxy1",
"3.5+galaxy1",
- "3.5+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.0+galaxy0",
- "4.8+galaxy1",
- "4.9+galaxy1",
- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
"3.5+galaxy0",
- "3.4+galaxy2",
"4.6+galaxy0",
- "3.4+galaxy1",
- "4.6+galaxy1",
- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
+ "4.8+galaxy0"
]
},
{
@@ -316001,7 +284418,7 @@
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"video_view": 0,
"visit_duration": 257,
- "visitors": 2249545,
+ "visitors": 2260397,
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@@ -316200,7 +284617,7 @@
],
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- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Essential genes detection with Transposon insertion sequencing",
"outputs": [
{
@@ -317987,20 +286404,6 @@
},
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- "contributions": {
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- ],
- "reviewing": [
- "bgruening",
- "shiltemann",
- "bebatut",
- "abretaud",
- "nsoranzo",
- "hexylena",
- "lecorguille"
- ]
- },
"contributors": [
{
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@@ -318026,194 +286429,21 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
"twitter": "abretau",
"url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
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- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "contact_for_training": true,
- "elixir_node": "fr",
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- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
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- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
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- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
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- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "gallantries",
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- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
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- "lon": 4.46
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-maker",
"edam_operation": [
- "Operation",
- "Genome assembly",
- "Sequence annotation",
- "Sequence assembly validation",
"Homology-based gene prediction",
+ "Genome assembly",
"Genome annotation",
+ "Sequence assembly validation",
+ "Sequence annotation",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Operation",
"Gene prediction",
"Ab-initio gene prediction",
- "Genome visualisation",
- "Scaffolding",
- "Transcriptome assembly"
+ "Genome visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -318248,7 +286478,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 22324,
+ "pageviews": 22451,
"priority": 4,
"pub_date": "2018-09-24",
"questions": [
@@ -318259,13 +286489,13 @@
"short_tools": [
"augustus_training",
"snap_training",
+ "maker",
+ "jcvi_gff_stats",
+ "maker_map_ids",
"fasta-stats",
"gffread",
"jbrowse",
- "jcvi_gff_stats",
- "maker_map_ids",
- "busco",
- "maker"
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -318328,6 +286558,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -318383,10 +286617,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -318433,11 +286663,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -318482,6 +286707,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -318535,10 +286764,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -318584,14 +286809,6 @@
"state": "exact",
"version": "3.3.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.4.0+galaxy1",
- "3.4.0+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -318637,6 +286854,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -318692,10 +286913,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -318741,14 +286958,6 @@
"state": "exact",
"version": "2.2.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1.3+galaxy0",
- "2.2.1.4+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -318798,6 +287007,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -318830,10 +287043,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -318856,10 +287069,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -318905,23 +287114,6 @@
"state": "exact",
"version": "4.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
- "5.2.2+galaxy2",
- "5.3.1+galaxy0",
- "5.3.2+galaxy0",
- "5.5.0+galaxy0",
- "5.2.2+galaxy0",
- "5.7.1+galaxy0",
- "5.8.0+galaxy0",
- "5.4.5+galaxy0",
- "5.2.2+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -318967,6 +287159,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -319025,169 +287221,157 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2.0"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0",
- "1.0.3"
- ]
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "1.0.1"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
- },
- {
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "1.16.9+galaxy0",
- "1.16.11+galaxy1"
- ]
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "inexact",
- "versions": [
- "1.16.11+galaxy1"
- ]
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.16.10+galaxy0"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.0.1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "inexact",
+ "versions": [
+ "1.16.9+galaxy0",
+ "1.16.11+galaxy1"
+ ]
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "inexact",
+ "versions": [
+ "1.16.11+galaxy1"
+ ]
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "1.16.10+galaxy0"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -319238,11 +287422,6 @@
"state": "exact",
"version": "1.16.10+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.10+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -319288,6 +287467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -319340,10 +287523,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -319387,11 +287566,6 @@
"state": "exact",
"version": "0.8.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -319437,6 +287611,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -319490,10 +287668,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -319539,14 +287713,6 @@
"state": "exact",
"version": "2.31.11"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11+galaxy1",
- "2.31.11+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -319592,6 +287758,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -319644,10 +287814,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -319691,11 +287857,6 @@
"state": "exact",
"version": "2.31.11"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.31.11"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -319741,6 +287902,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -319793,10 +287958,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -319840,10 +288001,6 @@
"state": "exact",
"version": "2013_11_29+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -319908,7 +288065,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 113,
- "visitors": 12168,
+ "visitors": 12246,
"workflows": [
{
"creators": [
@@ -320116,7 +288273,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Maker\"];\n 0 -->|output| 3;\n 2 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Fasta Statistics\"];\n 2 -->|output| 4;\n 2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n 4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n 5[\"Busco\"];\n 2 -->|output| 5;\n a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n 5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n 7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n 5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n 5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n 6[\"Train Augustus\"];\n 2 -->|output| 6;\n 3 -->|output_gff| 6;\n 7[\"Genome annotation statistics\"];\n 3 -->|output_gff| 7;\n 2 -->|output| 7;\n 2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n 7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n 71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n 7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n 8[\"gffread\"];\n 3 -->|output_gff| 8;\n 2 -->|output| 8;\n 9[\"Train SNAP\"];\n 2 -->|output| 9;\n 3 -->|output_gff| 9;\n 10[\"Busco\"];\n 8 -->|output_exons| 10;\n a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n 10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n 11[\"Maker\"];\n 6 -->|output_tar| 11;\n 9 -->|output| 11;\n 2 -->|output| 11;\n 3 -->|output_full| 11;\n 12[\"gffread\"];\n 11 -->|output_gff| 12;\n 2 -->|output| 12;\n 13[\"Train Augustus\"];\n 2 -->|output| 13;\n 11 -->|output_gff| 13;\n 42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n 13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n 14[\"Genome annotation statistics\"];\n 11 -->|output_gff| 14;\n 2 -->|output| 14;\n 9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n 14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n 61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n 14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n 15[\"Train SNAP\"];\n 2 -->|output| 15;\n 11 -->|output_gff| 15;\n 458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n 15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n 16[\"Busco\"];\n 12 -->|output_exons| 16;\n f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n 16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n 17[\"Maker\"];\n 13 -->|output_tar| 17;\n 15 -->|output| 17;\n 2 -->|output| 17;\n 11 -->|output_full| 17;\n 18[\"Map annotation ids\"];\n 17 -->|output_gff| 18;\n 63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n 18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n 19[\"JBrowse\"];\n 2 -->|output| 19;\n 3 -->|output_gff| 19;\n 18 -->|renamed| 19;\n 11 -->|output_gff| 19;\n 3 -->|output_evidences| 19;\n 11 -->|output_evidences| 19;\n 17 -->|output_evidences| 19;\n 5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n 19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n 20[\"gffread\"];\n 18 -->|renamed| 20;\n 2 -->|output| 20;\n 52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n 20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n 5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n 20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n 84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n 20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n 21[\"Genome annotation statistics\"];\n 18 -->|renamed| 21;\n 2 -->|output| 21;\n f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n 21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n 21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n 22[\"Busco\"];\n 20 -->|output_exons| 22;\n 0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n 22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome annotation with Maker ",
"outputs": [
{
@@ -321328,20 +289485,19 @@
],
"dir": "topics/genome-annotation/tutorials/functional",
"edam_operation": [
+ "Fold recognition",
"Homology-based gene prediction",
- "Genome annotation",
- "Sequence motif recognition",
"Protein feature detection",
- "Query and retrieval",
"Sequence alignment analysis",
- "Fold recognition",
- "Information extraction"
+ "Genome annotation",
+ "Query and retrieval",
+ "Information extraction",
+ "Sequence motif recognition"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -321367,7 +289523,7 @@
"objectives": [
"Perform functional annotation using EggNOG-mapper and InterProScan"
],
- "pageviews": 3759,
+ "pageviews": 3776,
"priority": 6,
"pub_date": "2022-07-20",
"questions": [
@@ -321375,10 +289531,10 @@
],
"short_id": "T00173",
"short_tools": [
- "eggnog_mapper",
- "interproscan",
"ncbi_blastp_wrapper",
- "bg_diamond"
+ "bg_diamond",
+ "eggnog_mapper",
+ "interproscan"
],
"slides": false,
"slides_recordings": false,
@@ -321395,11 +289551,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -321441,6 +289592,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -321496,10 +289651,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -321546,11 +289697,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -321595,6 +289741,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -321654,10 +289804,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -321700,11 +289846,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -321750,6 +289891,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -321802,10 +289947,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -321838,8 +289979,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "5.52-86.0+galaxy1",
- "5.54-87.0+galaxy2"
+ "5.54-87.0+galaxy2",
+ "5.52-86.0+galaxy1"
]
},
{
@@ -321852,11 +289993,6 @@
"state": "exact",
"version": "5.59-91.0+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.59-91.0+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -321902,6 +290038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -321936,8 +290076,8 @@
"state": "inexact",
"versions": [
"2.10.1+galaxy1",
- "2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.14.1+galaxy2"
]
},
{
@@ -321960,10 +290100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -322006,8 +290142,8 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.14.1+galaxy2",
"0.3.3",
+ "2.14.1+galaxy2",
"0.0.11",
"0.1.07",
"0.3.0"
@@ -322023,11 +290159,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -322075,6 +290206,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -322127,10 +290262,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -322180,11 +290311,6 @@
"state": "exact",
"version": "2.1.8+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.8+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -322244,7 +290370,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 101,
- "visitors": 2618,
+ "visitors": 2634,
"workflows": [
{
"creators": [
@@ -322307,7 +290433,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"eggNOG Mapper\"];\n 0 -->|output| 1;\n 2[\"InterProScan\"];\n 0 -->|output| 2;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Functional annotation",
"outputs": [
{
@@ -322799,7 +290925,7 @@
"Learn how to manually refine genome annotations within Apollo",
"Export refined genome annotations"
],
- "pageviews": 1667,
+ "pageviews": 1671,
"priority": 6,
"pub_date": "2022-08-22",
"questions": [
@@ -322826,9 +290952,9 @@
],
"short_id": "T00170",
"short_tools": [
- "iframe",
+ "jbrowse",
"create_or_update",
- "jbrowse"
+ "iframe"
],
"slides": false,
"slides_recordings": false,
@@ -322876,6 +291002,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -322931,10 +291061,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -322981,11 +291107,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -323030,6 +291151,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -323082,10 +291207,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -323132,10 +291253,6 @@
"4.2.13+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -323179,6 +291296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -323231,10 +291352,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -323279,10 +291396,6 @@
"state": "exact",
"version": "4.2.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -323326,6 +291439,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -323381,10 +291498,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -323420,23 +291533,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -323449,11 +291562,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -323513,7 +291621,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 155,
- "visitors": 981,
+ "visitors": 985,
"zenodo_link": "https://zenodo.org/record/3270822"
},
{
@@ -323776,11 +291884,11 @@
],
"dir": "topics/genome-annotation/tutorials/lncrna",
"edam_operation": [
- "RNA-Seq analysis",
"Classification",
+ "Annotation",
+ "RNA-Seq analysis",
"Sequence annotation",
- "Transcriptome assembly",
- "Annotation"
+ "Transcriptome assembly"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -323792,7 +291900,6 @@
"UseGalaxy.be",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -323819,7 +291926,7 @@
"Classify lncRNAs according to their location",
"Update genome annotation with lncRNAs"
],
- "pageviews": 1667,
+ "pageviews": 1683,
"priority": 7,
"pub_date": "2022-09-23",
"questions": [
@@ -323854,11 +291961,11 @@
],
"short_id": "T00177",
"short_tools": [
- "tp_cat",
"Extract_features1",
+ "stringtie",
+ "tp_cat",
"gffread",
- "feelnc",
- "stringtie"
+ "feelnc"
],
"slides": false,
"slides_recordings": false,
@@ -323881,11 +291988,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -323925,6 +292027,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -323980,10 +292086,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -324030,11 +292132,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -324079,6 +292176,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324131,10 +292232,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -324175,10 +292272,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -324221,6 +292314,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324275,10 +292372,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -324327,11 +292420,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -324377,6 +292465,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324401,8 +292493,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -324413,8 +292505,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
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- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -324437,10 +292529,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -324483,26 +292571,16 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
"server": "https://usegalaxy.eu",
"state": "inexact",
"versions": [
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"0.1.1",
- "9.3+galaxy1",
- "9.3+galaxy0"
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- "state": "inexact",
- "versions": [
"0.1.0",
- "0.1.1",
"9.3+galaxy1",
"9.3+galaxy0"
]
@@ -324511,16 +292589,16 @@
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "0.1.0",
"0.1.1",
+ "0.1.0",
"9.3+galaxy1"
]
},
@@ -324528,8 +292606,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "0.1.0",
"0.1.1",
+ "0.1.0",
"9.3+galaxy1",
"9.3+galaxy0"
]
@@ -324564,6 +292642,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324619,10 +292701,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -324656,10 +292734,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -324672,11 +292750,6 @@
"state": "exact",
"version": "2.2.1.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -324722,6 +292795,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324777,10 +292854,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -324814,10 +292887,10 @@
"state": "inexact",
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- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -324832,11 +292905,6 @@
"state": "exact",
"version": "2.2.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -324886,6 +292954,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -324938,10 +293010,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -324987,11 +293055,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -325039,6 +293102,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -325091,10 +293158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -325128,8 +293191,8 @@
"state": "inexact",
"versions": [
"0.1.1.1",
- "0.1.1",
- "0.2"
+ "0.2",
+ "0.1.1"
]
},
{
@@ -325144,16 +293207,8 @@
"state": "inexact",
"versions": [
"0.1.1.1",
- "0.1.1",
- "0.2",
- "0.2.1+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
"0.2",
+ "0.1.1",
"0.2.1+galaxy0"
]
},
@@ -325211,6 +293266,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -325264,10 +293323,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -325316,11 +293371,6 @@
"state": "exact",
"version": "1.3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -325343,9 +293393,9 @@
"2.1.1",
"1.3.4",
"2.2.1+galaxy1",
- "1.3.3.1",
"2.1.7+galaxy1",
"2.1.7",
+ "1.3.3.1",
"2.2.3+galaxy0"
]
},
@@ -325379,6 +293429,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -325434,10 +293488,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -325474,10 +293524,10 @@
"state": "inexact",
"versions": [
"1.3.6",
- "1.3.3",
+ "1.0.0",
"2.1.1",
"1.3.4",
- "1.0.0"
+ "1.3.3"
]
},
{
@@ -325493,34 +293543,20 @@
"versions": [
"1.3.6",
"2.2.1+galaxy0",
- "1.3.3",
+ "1.0.0",
"2.1.1",
"1.3.4",
- "1.0.0",
+ "1.3.3",
"2.2.1+galaxy1",
- "1.1.0",
- "1.2.3",
- "1.0.3",
- "1.3.3.1",
"2.1.7+galaxy1",
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- "2.1.7",
- "2.2.2+galaxy0",
"1.0.4",
- "2.2.3+galaxy0"
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
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- "2.1.1",
- "2.2.1+galaxy1",
- "2.1.7+galaxy1",
- "2.1.7",
"2.2.2+galaxy0",
+ "2.1.7",
+ "1.0.1",
+ "1.1.0",
+ "1.0.3",
+ "1.2.3",
+ "1.3.3.1",
"2.2.3+galaxy0"
]
},
@@ -325539,16 +293575,16 @@
"versions": [
"1.3.6",
"2.2.1+galaxy0",
- "1.3.3",
"2.1.1",
"1.3.4",
+ "1.3.3",
"2.2.1+galaxy1",
+ "2.1.7+galaxy1",
+ "2.2.2+galaxy0",
"1.1.0",
- "1.2.3",
"1.0.3",
+ "1.2.3",
"1.3.3.1",
- "2.1.7+galaxy1",
- "2.2.2+galaxy0",
"2.2.3+galaxy0",
"1.3.3.2"
]
@@ -325561,9 +293597,9 @@
"2.1.1",
"1.3.4",
"2.2.1+galaxy1",
- "1.3.3.1",
"2.1.7+galaxy1",
"2.1.7",
+ "1.3.3.1",
"2.2.3+galaxy0"
]
},
@@ -325612,8 +293648,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 133,
- "visitors": 1228,
+ "visit_duration": 131,
+ "visitors": 1239,
"workflows": [
{
"creators": [
@@ -325740,7 +293776,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"StringTie\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"gffread\"];\n 1 -->|output| 4;\n 5[\"FEELnc\"];\n 3 -->|output_gtf| 5;\n 2 -->|output| 5;\n 4 -->|output_gtf| 5;\n 4055b259-173c-492d-86a4-5e662b663421[\"Output\\nmRNAs\"];\n 5 --> 4055b259-173c-492d-86a4-5e662b663421;\n style 4055b259-173c-492d-86a4-5e662b663421 stroke:#2c3143,stroke-width:4px;\n abc029ba-b7ba-4586-88b4-5e5d758c2f39[\"Output\\nlncRNAs\"];\n 5 --> abc029ba-b7ba-4586-88b4-5e5d758c2f39;\n style abc029ba-b7ba-4586-88b4-5e5d758c2f39 stroke:#2c3143,stroke-width:4px;\n 93ff3464-d1bb-4059-86af-3e703da3e542[\"Output\\nClassifier output\"];\n 5 --> 93ff3464-d1bb-4059-86af-3e703da3e542;\n style 93ff3464-d1bb-4059-86af-3e703da3e542 stroke:#2c3143,stroke-width:4px;\n 6[\"Concatenate datasets\"];\n 4 -->|output_gtf| 6;\n 5 -->|candidate_lncRNA| 6;\n 7b91b6a4-ef67-4359-9c93-eabcc021b0fc[\"Output\\nfinal_annotation\"];\n 6 --> 7b91b6a4-ef67-4359-9c93-eabcc021b0fc;\n style 7b91b6a4-ef67-4359-9c93-eabcc021b0fc stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
"outputs": [
{
@@ -326019,19 +294055,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_count\n owner: iuc\n revisions: e329d44424d7\n tool_panel_section_label: Genome Editing\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_mle\n owner: iuc\n revisions: 26126538a86f\n tool_panel_section_label: Genome Editing\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_test\n owner: iuc\n revisions: 9b4f4533c9ee\n tool_panel_section_label: Genome Editing\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: 9a913cdee30e\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: 75c93c70d094\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: volcanoplot\n owner: iuc\n revisions: 83c573f2e73c\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 4e5056fefd88\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: de6cebe3c043\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json",
- "contributions": {
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- "mblue9",
- "kenjifujihara",
- "twishigulati"
- ],
- "reviewing": [
- "bgruening",
- "hexylena",
- "abretaud",
- "shiltemann"
- ]
- },
"contributors": [
{
"id": "mblue9",
@@ -326056,140 +294079,21 @@
"name": "Twishi Gulati",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/twishigulati/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/twishigulati.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
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- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/genome-annotation/tutorials/crispr-screen",
"edam_operation": [
+ "Genetic variation analysis",
+ "Validation",
+ "Read pre-processing",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Primer removal",
- "Validation",
- "Genetic variation analysis",
"Sequence composition calculation",
+ "Primer removal",
"Sequence trimming"
],
"edam_topic": [],
"exact_supported_servers": [
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -326218,7 +294122,7 @@
"Identify differentially enriched genes across conditions",
"Generate volcano plot to visualise results"
],
- "pageviews": 4808110,
+ "pageviews": 4831232,
"priority": 8,
"pub_date": "2021-10-15",
"questions": [
@@ -326263,14 +294167,14 @@
],
"short_id": "T00171",
"short_tools": [
+ "mageck_mle",
"fastqc",
- "mageck_count",
+ "multiqc",
"tp_awk_tool",
"cutadapt",
- "mageck_mle",
- "multiqc",
"volcanoplot",
- "mageck_test"
+ "mageck_test",
+ "mageck_count"
],
"slides": true,
"slides_recordings": [
@@ -326290,11 +294194,6 @@
"subtopic": "eukaryote",
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -326351,6 +294250,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -326406,10 +294309,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -326456,11 +294355,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -326505,6 +294399,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -326559,10 +294457,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -326609,11 +294503,6 @@
"state": "exact",
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- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -326660,177 +294549,7 @@
"state": "missing"
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- "state": "exact",
- "version": "0.72+galaxy1"
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- "versions": [
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- {
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- "state": "missing"
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- "version": "0.72+galaxy1"
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- "state": "inexact",
- "versions": [
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- "state": "inexact",
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- "0.62"
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
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- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.72+galaxy1"
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- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "0.72+galaxy1"
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- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
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- "version": "0.72+galaxy1"
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- "servers": [
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -326856,7 +294575,7 @@
{
"server": "https://galaxy.mesocentre.uca.fr",
"state": "exact",
- "version": "0.73+galaxy0"
+ "version": "0.72+galaxy1"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -326868,7 +294587,7 @@
{
"server": "https://galaxytrakr.org/",
"state": "exact",
- "version": "0.73+galaxy0"
+ "version": "0.72+galaxy1"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -326891,7 +294610,172 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0",
+ "0.69",
+ "0.65",
+ "0.68",
+ "0.52",
+ "0.67",
+ "0.63",
+ "0.64",
+ "0.62"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "0.72+galaxy1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.72+galaxy1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "0.73+galaxy0"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "0.73+galaxy0"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -326919,8 +294803,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -326944,12 +294828,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -326959,9 +294843,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -326972,11 +294856,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327022,6 +294901,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327074,10 +294957,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -327123,18 +295002,13 @@
"state": "inexact",
"versions": [
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- "0.5.7.3",
- "0.5.7.1",
- "0.5.7.2",
"0.5.7",
- "0.5.7.4"
+ "0.5.7.1",
+ "0.5.7.3",
+ "0.5.7.4",
+ "0.5.7.2"
]
},
- {
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- "state": "exact",
- "version": "0.5.9.2.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327180,6 +295054,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327232,10 +295110,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -327285,11 +295159,6 @@
"0.5.7"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.9.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327335,6 +295204,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327387,10 +295260,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -327436,15 +295305,10 @@
"state": "inexact",
"versions": [
"0.5.8.1",
- "0.5.7.1",
- "0.5.7"
+ "0.5.7",
+ "0.5.7.1"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.9.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327490,6 +295354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327544,10 +295412,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -327600,11 +295464,6 @@
"state": "exact",
"version": "1.11+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327650,6 +295509,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327675,9 +295538,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -327709,10 +295572,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -327765,11 +295624,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327815,6 +295669,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -327872,10 +295730,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -327910,8 +295764,8 @@
"state": "inexact",
"versions": [
"0.0.3",
- "0.0.2",
- "0.0.1"
+ "0.0.1",
+ "0.0.2"
]
},
{
@@ -327924,11 +295778,6 @@
"state": "exact",
"version": "0.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -327974,6 +295823,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -328013,8 +295866,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -328037,10 +295890,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -328083,8 +295932,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -328099,11 +295948,6 @@
"state": "exact",
"version": "3.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -328151,6 +295995,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -328190,8 +296038,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -328214,10 +296062,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -328260,8 +296104,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -328276,11 +296120,6 @@
"state": "exact",
"version": "3.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -328349,7 +296188,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 273,
- "visitors": 1839664,
+ "visitors": 1849816,
"workflows": [
{
"creators": [],
@@ -328459,7 +296298,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nbroadgpp-brunello-library-contents.csv\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCalabrese_SetA_Guides_Reference.csv\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"FastQC\"];\n 2 -->|output| 3;\n 4[\"Cutadapt\"];\n 2 -->|output| 4;\n 5[\"MultiQC\"];\n 3 -->|text_file| 5;\n 6[\"MAGeCK count\"];\n 4 -->|out1| 6;\n 7[\"MAGeCKs test\"];\n 6 -->|counts| 7;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Workflow constructed from history 'CRISPR tutorial Kenji'",
"outputs": [],
"parent_id": "genome-annotation/crispr-screen",
@@ -328522,25 +296361,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n owner: crs4\n revisions: bf68eb663bc3\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n owner: crs4\n revisions: 111884f0d912\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions: a6e57ff585c0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
- "contributions": {
- "authorship": [
- "annasyme",
- "tseemann",
- "slugger70"
- ],
- "reviewing": [
- "bgruening",
- "hexylena",
- "shiltemann",
- "bebatut",
- "abretaud",
- "annasyme",
- "nsoranzo",
- "slugger70",
- "njall",
- "mblue9"
- ]
- },
"contributors": [
{
"id": "annasyme",
@@ -328571,202 +296391,6 @@
"orcid": "0000-0002-6100-4385",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "id": "annasyme",
- "joined": "2017-09",
- "name": "Anna Syme",
- "orcid": "0000-0002-9906-0673",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "elixir_node": "au",
- "email": "simon.gladman@unimelb.edu.au",
- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
- "orcid": "0000-0002-6100-4385",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
- },
- {
- "id": "mblue9",
- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
@@ -328777,9 +296401,9 @@
"topic_0080"
],
"edam_operation": [
- "Coding region prediction",
"Genome annotation",
"Genome visualisation",
+ "Coding region prediction",
"Gene prediction"
],
"edam_topic": [
@@ -328811,7 +296435,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -328832,7 +296455,7 @@
"Annotate genome with Prokka",
"View annotations in JBrowse"
],
- "pageviews": 6207675,
+ "pageviews": 6230726,
"pub_date": "2018-03-06",
"questions": [
"How can we annotate a bacterial genome?",
@@ -328854,8 +296477,8 @@
],
"short_id": "T00168",
"short_tools": [
- "prokka",
- "jbrowse"
+ "jbrowse",
+ "prokka"
],
"slides": true,
"slides_recordings": [
@@ -328912,11 +296535,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -328951,6 +296569,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -329006,10 +296628,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -329056,11 +296674,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -329105,6 +296718,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -329163,10 +296780,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -329218,15 +296831,6 @@
"state": "exact",
"version": "1.14.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.14.6+galaxy1",
- "1.13",
- "1.14.5+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -329274,6 +296878,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -329332,10 +296940,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -329387,11 +296991,6 @@
"state": "exact",
"version": "1.14.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.14.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -329407,8 +297006,8 @@
"state": "inexact",
"versions": [
"1.14.6+galaxy1",
- "1.14.5",
"1.12.0",
+ "1.14.5",
"1.14.6+galaxy0"
]
},
@@ -329442,6 +297041,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -329497,10 +297100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -329536,23 +297135,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -329565,11 +297164,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -329628,7 +297222,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 262,
- "visitors": 2258940,
+ "visitors": 2269815,
"workflows": [
{
"creators": [
@@ -329759,7 +297353,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Prokka\"];\n 0 -->|output| 1;\n a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n 1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n 2[\"JBrowse\"];\n 1 -->|out_fna| 2;\n 1 -->|out_gff| 2;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome Annotation with Prokka ",
"outputs": [
{
@@ -330076,8 +297670,8 @@
],
"short_id": "T00152",
"short_tools": [
- "intermine",
- "galaxy_intermine_exchange"
+ "galaxy_intermine_exchange",
+ "intermine"
],
"slides": false,
"slides_recordings": false,
@@ -330139,6 +297733,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -330194,10 +297792,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -330244,11 +297838,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -330293,6 +297882,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -330345,10 +297938,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -330389,10 +297978,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -330435,6 +298020,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -330487,10 +298076,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -330534,10 +298119,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -330652,7 +298233,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Create InterMine Interchange\"];\n 0 -->|output| 1;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Intermine import/export",
"outputs": [
{
@@ -330914,24 +298495,6 @@
},
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- "contributions": {
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- "delphine-l",
- "hexylena"
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- "reviewing": [
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- "bgruening",
- "hexylena",
- "abretaud",
- "nsoranzo",
- "nekrut",
- "njall",
- "mblue9"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -330978,191 +298541,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- "elixir-europe"
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- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "contact_for_training": true,
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- "lon": -1.64
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
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- },
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- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
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- "email": "anton@nekrut.org",
- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
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- "name": "Maria Doyle",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/assembly/tutorials/ecoli_comparison",
@@ -331172,11 +298550,11 @@
"topic_3301"
],
"edam_operation": [
+ "Sequence visualisation",
"Read mapping",
"Mapping",
- "Genome visualisation",
"Sequence alignment",
- "Sequence visualisation"
+ "Genome visualisation"
],
"edam_topic": [
"Sequence assembly",
@@ -331207,7 +298585,7 @@
"Perform sequence comparison to locate rearrangements",
"Identify genes located in deletions"
],
- "pageviews": 12347,
+ "pageviews": 12361,
"pub_date": "2018-06-14",
"questions": [
"I just assembled a genome. How does it compare with already sequenced genomes?",
@@ -331224,33 +298602,33 @@
],
"short_id": "T00032",
"short_tools": [
+ "cat1",
+ "tp_sort_header_tool",
+ "Filter1",
+ "Cut1",
+ "mergeCols1",
+ "fasta_compute_length",
+ "Grep1",
+ "tp_replace_in_line",
"bedtools_complementbed",
- "datamash_ops",
- "tp_cat",
"tp_replace_in_column",
- "tp_replace_in_line",
+ "tp_cat",
+ "tp_grep_tool",
+ "lastz_wrapper_2",
+ "random_lines1",
+ "datamash_ops",
"jbrowse",
- "tp_sort_header_tool",
- "upload1",
+ "addValue",
+ "circos",
+ "tp_sed_tool",
+ "bedtools_intersectbed",
+ "collapse_dataset",
"circos_aln_to_links",
"circos_interval_to_tiles",
"fasta_filter_by_length",
- "bedtools_sortbed",
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"join1",
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- "lastz_wrapper_2",
- "cat1",
- "circos",
- "mergeCols1",
- "fasta_compute_length",
- "bedtools_intersectbed"
+ "upload1",
+ "bedtools_sortbed"
],
"slides": false,
"slides_recordings": false,
@@ -331280,6 +298658,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -331335,10 +298717,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -331385,11 +298763,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -331435,287 +298808,7 @@
"state": "local"
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -331748,7 +298841,7 @@
},
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"server": "https://galaxytrakr.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -331771,9 +298864,143 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Filter1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
"state": "local"
},
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -331815,7 +299042,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Grep1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -331860,6 +299221,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -331912,10 +299277,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -331956,10 +299317,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -332002,6 +299359,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -332054,10 +299415,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -332098,10 +299455,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -332144,6 +299497,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -332196,10 +299553,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -332240,10 +299593,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -332286,6 +299635,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -332340,10 +299693,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -332390,11 +299739,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -332440,6 +299784,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -332494,10 +299842,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -332544,11 +299888,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -332594,6 +299933,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -332648,10 +299991,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -332698,11 +300037,6 @@
"state": "exact",
"version": "1.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -332748,6 +300082,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -332802,10 +300140,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -332852,11 +300186,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -332902,6 +300231,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -332956,10 +300289,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -333006,11 +300335,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -333056,6 +300380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333110,10 +300438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -333160,11 +300484,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -333210,6 +300529,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333263,10 +300586,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -333313,11 +300632,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -333362,6 +300676,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333417,10 +300735,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -333470,15 +300784,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3",
- "1.0.2",
- "1.0.4"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -333531,6 +300836,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333583,10 +300892,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -333635,11 +300940,6 @@
"state": "exact",
"version": "1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -333687,6 +300987,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333739,10 +301043,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -333787,11 +301087,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -333837,6 +301132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -333891,10 +301190,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -333932,8 +301227,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.04.15+galaxy0",
- "1.04.22+galaxy0"
+ "1.04.22+galaxy0",
+ "1.04.15+galaxy0"
]
},
{
@@ -333941,11 +301236,6 @@
"state": "exact",
"version": "1.3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -333991,6 +301281,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334043,10 +301337,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -334090,13 +301380,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -334143,6 +301426,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334200,16 +301487,12 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
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- "2.31.1+galaxy0"
+ "2.31.1+galaxy0",
+ "2.30.0+galaxy1"
]
},
{
@@ -334258,17 +301541,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
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- "2.30.0+galaxy1",
- "2.31.1+galaxy0",
- "2.29.0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -334318,6 +301590,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334375,10 +301651,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -334424,9 +301696,9 @@
"2.29.2",
"2.30.0",
"2.30.0+galaxy1",
- "2.27.1+galaxy1",
"2.19.0",
- "2.29.0"
+ "2.29.0",
+ "2.27.1+galaxy1"
]
},
{
@@ -334434,17 +301706,6 @@
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},
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- "2.31.1+galaxy0",
- "2.30.0+galaxy1",
- "2.29.0"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -334494,6 +301755,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334527,8 +301792,8 @@
"server": "https://galaxytrakr.org/",
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"versions": [
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- "2.30.0"
+ "2.30.0",
+ "2.29.2"
]
},
{
@@ -334551,10 +301816,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -334597,8 +301858,8 @@
"state": "inexact",
"versions": [
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- "2.29.2",
"2.30.0",
+ "2.29.2",
"2.30.0+galaxy2",
"2.29.0",
"2.19.0",
@@ -334610,23 +301871,12 @@
"state": "exact",
"version": "2.27.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
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- "versions": [
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- "2.30.0",
- "2.31.1+galaxy0",
- "2.30.0+galaxy2",
- "2.29.0"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.29.2",
"2.30.0",
+ "2.29.2",
"2.19.0"
]
},
@@ -334670,6 +301920,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334726,10 +301980,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -334782,11 +302032,6 @@
"0.69.8+galaxy10"
]
},
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- "state": "exact",
- "version": "0.69.8+galaxy7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -334832,6 +302077,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -334888,10 +302137,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -334940,11 +302185,6 @@
"state": "exact",
"version": "0.69.8+galaxy7"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.69.8+galaxy7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -334990,6 +302230,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -335042,10 +302286,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -335086,10 +302326,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -335132,6 +302368,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -335189,10 +302429,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -335239,11 +302475,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -335289,6 +302520,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -335352,10 +302587,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -335404,11 +302635,6 @@
"state": "exact",
"version": "1.16.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -335458,6 +302684,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -335483,8 +302713,8 @@
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -335518,10 +302748,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -335571,21 +302797,13 @@
"state": "exact",
"version": "4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -335628,6 +302846,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -335684,10 +302906,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -335737,14 +302955,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -335790,6 +303000,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -335842,10 +303056,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -335886,10 +303096,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -335971,7 +303177,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 180,
- "visitors": 6194,
+ "visitors": 6204,
"workflows": [
{
"creators": [],
@@ -336161,7 +303367,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Collapse Collection\"];\n 6 -->|output| 10;\n 11[\"Text transformation\"];\n 7 -->|output| 11;\n 12[\"Add column\"];\n 8 -->|out_file1| 12;\n 13[\"LASTZ\"];\n 9 -->|output| 13;\n 3 -->|output| 13;\n 14[\"random_lines1\"];\n 10 -->|output| 14;\n 15[\"Filter\"];\n 10 -->|output| 15;\n 16[\"Search in textfiles\"];\n 11 -->|output| 16;\n 17[\"Concatenate datasets\"];\n 11 -->|output| 17;\n 9 -->|output| 17;\n 18[\"Cut\"];\n 12 -->|out_file1| 18;\n 19[\"Text transformation\"];\n 13 -->|output| 19;\n 2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 20[\"Datamash\"];\n 15 -->|out_file1| 20;\n 21[\"Compute sequence length\"];\n 17 -->|out_file1| 21;\n 22[\"Collapse Collection\"];\n 18 -->|out_file1| 22;\n 23[\"Merge Columns\"];\n 19 -->|output| 23;\n 24[\"Select\"];\n 20 -->|out_file| 24;\n 25[\"Sort\"];\n 21 -->|output| 25;\n 26[\"Collapse Collection\"];\n 23 -->|out_file1| 26;\n 27[\"Cut\"];\n 26 -->|output| 27;\n 28[\"Cut\"];\n 26 -->|output| 28;\n 29[\"Concatenate datasets\"];\n 27 -->|out_file1| 29;\n 28 -->|out_file1| 29;\n 3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 30[\"SortBED\"];\n 29 -->|out_file1| 30;\n 31[\"ComplementBed\"];\n 25 -->|outfile| 31;\n 30 -->|output| 31;\n 32[\"Filter\"];\n 31 -->|output| 32;\n 33[\"Filter\"];\n 32 -->|out_file1| 33;\n 34[\"Intersect intervals\"];\n 33 -->|out_file1| 34;\n 22 -->|output| 34;\n 35[\"Join two Datasets\"];\n 34 -->|output| 35;\n 1 -->|output| 35;\n 4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Filter sequences by length\"];\n 0 -->|output| 5;\n 6[\"LASTZ\"];\n 2 -->|output| 6;\n 0 -->|output| 6;\n 7[\"Collapse Collection\"];\n 3 -->|output| 7;\n 8[\"Select\"];\n 4 -->|output| 8;\n 9[\"Text transformation\"];\n 5 -->|output| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Ecoli Comparison",
"outputs": [],
"parent_id": "assembly/ecoli_comparison",
@@ -336232,26 +303438,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n owner: iuc\n revisions: 836d1aa3e89a\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n owner: iuc\n revisions: c9a8ef2aa380\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
- "contributions": {
- "authorship": [
- "annasyme",
- "slugger70",
- "tseemann"
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- "reviewing": [
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- "hexylena",
- "bgruening",
- "shiltemann",
- "bebatut",
- "abretaud",
- "nsoranzo",
- "slugger70",
- "pvanheus",
- "njall",
- "mblue9"
- ]
- },
"contributors": [
{
"id": "annasyme",
@@ -336282,223 +303468,6 @@
"name": "Torsten Seemann",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
- },
- {
- "contact_for_training": true,
- "email": "jen@galaxyproject.org",
- "id": "jennaj",
- "joined": "2018-06",
- "linkedin": "jennifer.hillman.jackson",
- "location": {
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- "lat": 36.969918,
- "lon": -122.0226576
- },
- "maintainer_contact": "https://help.galaxyproject.org/",
- "matrix": "jennaj:matrix.org",
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- "orcid": "0000-0003-4012-8116",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jennaj/",
- "twitter": "jennaj_io",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/jennaj.json"
- },
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
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- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
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- "linkedin": "bgruening",
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- "lat": 47.997791,
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- "matrix": "bgruening:matrix.org",
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- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "bio": "Researcher at Erasmus Medical Center",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "id": "slugger70",
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- "joined": "2017-09",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
- "twitter": "pvanheus",
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- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
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- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/variant-analysis/tutorials/microbial-variants",
@@ -336511,9 +303480,9 @@
"topic_0199"
],
"edam_operation": [
+ "Phylogenetic tree visualisation",
"Genome visualisation",
"Variant calling",
- "Phylogenetic tree visualisation",
"Phylogenetic tree generation"
],
"edam_topic": [
@@ -336536,7 +303505,6 @@
"inexact_supported_servers": [
"GalaxyTrakr",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -336558,15 +303526,15 @@
"Determine the effect of those variants on genomic features",
"Understand if the SNP is potentially affecting the phenotype"
],
- "pageviews": 21232,
+ "pageviews": 21278,
"pub_date": "2018-02-26",
"questions": [
"How do we detect differences between a set of reads from a microorganism and a reference genome"
],
"short_id": "T00313",
"short_tools": [
- "snippy",
- "jbrowse"
+ "jbrowse",
+ "snippy"
],
"slides": false,
"slides_recordings": false,
@@ -336600,11 +303568,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -336639,6 +303602,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -336694,10 +303661,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -336744,11 +303707,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -336793,6 +303751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -336856,10 +303818,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -336894,193 +303852,175 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
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- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
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- ]
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- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.7.0.3"
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
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- "1.16.11+galaxy1",
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- "1.16.8+galaxy1",
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- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "1.16.9+galaxy0",
- "1.16.11+galaxy1",
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- "state": "exact",
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- "server": "https://usegalaxy.org.au",
- "state": "exact",
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- "state": "missing"
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- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "3.2"
+ "version": "0.7.0.3"
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "4.6.0+galaxy0"
+ "1.16.11+galaxy1"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "0.7.0.3"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.16.9+galaxy0",
+ "1.16.11+galaxy1",
+ "1.16.10+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.7.0.3"
+ },
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+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "0.7.0.3"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ "version": "0.7.0.3"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
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+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
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+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
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+ "4.6.0+galaxy0",
+ "4.5.0"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
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+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
"version": "3.2"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
"4.6.0+galaxy0"
]
},
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "3.2"
+ },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -337096,8 +304036,8 @@
"state": "inexact",
"versions": [
"4.5.0+galaxy1",
- "4.5.0",
- "4.6.0+galaxy0"
+ "4.6.0+galaxy0",
+ "4.5.0"
]
},
{
@@ -337142,7 +304082,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 119,
- "visitors": 12921,
+ "visitors": 12950,
"workflows": [
{
"creators": [],
@@ -337153,7 +304093,7 @@
"report": null,
"subworkflows": false
},
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{
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@@ -337324,8 +304264,8 @@
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],
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"name": "Microbial Variant Calling",
"outputs": [
{
@@ -337412,12 +304352,12 @@
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"label": "snippy_fasta",
"output_name": "snpconsensus",
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},
{
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}
]
},
@@ -337473,7 +304413,7 @@
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"label": "jbrowse_html",
"output_name": "output",
- "uuid": "94ef28fa-3df6-4bbd-9219-ff0b44eb9e90"
+ "uuid": "72d2c9b1-09c5-4169-b8e7-cde04bb1e8aa"
}
]
}
@@ -337911,7 +304851,7 @@
"Learn how to manually refine genome annotations within Apollo",
"Export refined genome annotations"
],
- "pageviews": 5401706,
+ "pageviews": 5424682,
"pub_date": "2021-06-04",
"questions": [
"How to visualize your genome after automated annotations have been performed?",
@@ -337952,10 +304892,10 @@
"short_id": "T00169",
"short_tools": [
"create_account",
- "jbrowse",
- "iframe",
"create_or_update",
- "list_organism"
+ "list_organism",
+ "jbrowse",
+ "iframe"
],
"slides": true,
"slides_recordings": [
@@ -338015,6 +304955,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -338070,10 +305014,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -338120,11 +305060,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -338169,6 +305104,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -338221,10 +305160,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -338269,10 +305204,6 @@
"state": "exact",
"version": "3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -338318,6 +305249,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -338370,10 +305305,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -338420,10 +305351,6 @@
"4.2.13+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -338468,150 +305395,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "4.2.13+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "4.2.5"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "4.2.5"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "4.2.5"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -338666,10 +305450,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -338712,12 +305492,151 @@
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "3.1"
+ "version": "4.2.5"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "4.2.5"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "missing"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "4.2.5"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
},
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "4.2.13+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "3.1"
+ },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -338763,6 +305682,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -338818,10 +305741,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -338857,23 +305776,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -338886,11 +305805,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -338952,7 +305866,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 313,
- "visitors": 2014123,
+ "visitors": 2024178,
"workflows": [
{
"creators": [],
@@ -339143,7 +306057,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Register Account\"];\n 5[\"List Organisms\"];\n 6[\"JBrowse\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 3 -->|output| 6;\n 2 -->|output| 6;\n 7[\"Create or Update Organism\"];\n 6 -->|output| 7;\n 8[\"Annotate\"];\n 7 -->|output| 8;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Apollo Load Test",
"outputs": [
{
@@ -340076,9 +306990,9 @@
"topic_4013"
],
"edam_operation": [
+ "Read mapping",
"Genome annotation",
- "Genome visualisation",
- "Read mapping"
+ "Genome visualisation"
],
"edam_topic": [
"Whole genome sequencing",
@@ -340091,8 +307005,7 @@
],
"exact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -340135,7 +307048,7 @@
"Get information about ARGs",
"Visualize the ARGs and plasmid genes in their genomic context"
],
- "pageviews": 2195,
+ "pageviews": 2256,
"pub_date": "2024-01-23",
"questions": [
"Which resistance genes are on a bacterial genome?",
@@ -340160,11 +307073,11 @@
"short_tools": [
"staramr_search",
"Grep1",
- "bakta",
- "bowtie2",
- "jbrowse",
"tbl2gff3",
- "upload1"
+ "upload1",
+ "jbrowse",
+ "bakta",
+ "bowtie2"
],
"slides": false,
"slides_recordings": false,
@@ -340180,11 +307093,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -340222,6 +307130,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -340277,10 +307189,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -340327,11 +307235,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -340376,6 +307279,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -340428,10 +307335,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -340472,10 +307375,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -340518,6 +307417,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -340542,9 +307445,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -340556,9 +307459,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -340582,10 +307485,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -340621,13 +307520,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -340641,17 +307540,12 @@
"state": "exact",
"version": "2.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.4.5+galaxy1",
"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -340698,6 +307592,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -340751,10 +307649,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -340797,11 +307691,6 @@
"state": "exact",
"version": "1.8.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -340851,6 +307740,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -340906,10 +307799,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -340945,23 +307834,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -340974,11 +307863,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -341024,6 +307908,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -341077,10 +307965,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -341123,11 +308007,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -341172,6 +308051,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -341206,10 +308089,10 @@
"state": "inexact",
"versions": [
"0.7.2+galaxy0",
+ "0.9.1+galaxy0",
"0.5.1",
- "0.2.1",
"0.8.0+galaxy0",
- "0.9.1+galaxy0"
+ "0.2.1"
]
},
{
@@ -341232,10 +308115,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -341281,11 +308160,6 @@
"state": "exact",
"version": "0.10.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.10.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -341335,6 +308209,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -341387,10 +308265,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -341431,10 +308305,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -341495,8 +308365,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 205,
- "visitors": 1603,
+ "visit_duration": 203,
+ "visitors": 1652,
"workflows": [
{
"creators": [
@@ -341518,7 +308388,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n 2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n 3[label=\"staramr\"]\n 0 -> 3 [label=\"output\"]\n k2f01e653531f44fe85a7b699a47ab683[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n 3 -> k2f01e653531f44fe85a7b699a47ab683\n 4[label=\"Bakta\"]\n 0 -> 4 [label=\"output\"]\n k4a680ee078c44733b9f0cb1a0ebcb174[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n 4 -> k4a680ee078c44733b9f0cb1a0ebcb174\n 5[label=\"Bowtie2\"]\n 1 -> 5 [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n ka3c861ca77bf41188f3ec452427aac79[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n 5 -> ka3c861ca77bf41188f3ec452427aac79\n 6[label=\"Select\"]\n 3 -> 6 [label=\"detailed_summary\"]\n 7[label=\"Table to GFF3\"]\n 6 -> 7 [label=\"out_file1\"]\n 8[label=\"JBrowse\"]\n 4 -> 8 [label=\"annotation_gff3\"]\n 7 -> 8 [label=\"output\"]\n 5 -> 8 [label=\"output\"]\n kcf90b47e652b428e817011929768a4d6[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n 8 -> kcf90b47e652b428e817011929768a4d6\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n 2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n 3[label=\"staramr\"]\n 0 -> 3 [label=\"output\"]\n k80c90033b1134ab0aa74bc854226af75[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n 3 -> k80c90033b1134ab0aa74bc854226af75\n 4[label=\"Bakta\"]\n 0 -> 4 [label=\"output\"]\n k136fe6f95bed4cfaa22693d7b18553a2[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n 4 -> k136fe6f95bed4cfaa22693d7b18553a2\n 5[label=\"Bowtie2\"]\n 1 -> 5 [label=\"output\"]\n 2 -> 5 [label=\"output\"]\n 0 -> 5 [label=\"output\"]\n kf33376aed46846b68c9f681067c2051e[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n 5 -> kf33376aed46846b68c9f681067c2051e\n 6[label=\"Select\"]\n 3 -> 6 [label=\"detailed_summary\"]\n 7[label=\"Table to GFF3\"]\n 6 -> 7 [label=\"out_file1\"]\n 8[label=\"JBrowse\"]\n 4 -> 8 [label=\"annotation_gff3\"]\n 7 -> 8 [label=\"output\"]\n 5 -> 8 [label=\"output\"]\n k20eae6766d394ec3a83dab27abd3ab91[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n 8 -> k20eae6766d394ec3a83dab27abd3ab91\n}",
"history": [
{
"hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
@@ -341633,8 +308503,8 @@
}
],
"license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"staramr\"];\n 0 -->|output| 3;\n 2f01e653-531f-44fe-85a7-b699a47ab683[\"Output\\nstararm_detailed_summary\"];\n 3 --> 2f01e653-531f-44fe-85a7-b699a47ab683;\n style 2f01e653-531f-44fe-85a7-b699a47ab683 stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174[\"Output\\nbakta_annotation_summary\"];\n 4 --> 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174;\n style 4a680ee0-78c4-4733-b9f0-cb1a0ebcb174 stroke:#2c3143,stroke-width:4px;\n 5[\"Bowtie2\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n a3c861ca-77bf-4118-8f3e-c452427aac79[\"Output\\nbowtie_mapping_stats\"];\n 5 --> a3c861ca-77bf-4118-8f3e-c452427aac79;\n style a3c861ca-77bf-4118-8f3e-c452427aac79 stroke:#2c3143,stroke-width:4px;\n 6[\"Select\"];\n 3 -->|detailed_summary| 6;\n 7[\"Table to GFF3\"];\n 6 -->|out_file1| 7;\n 8[\"JBrowse\"];\n 4 -->|annotation_gff3| 8;\n 7 -->|output| 8;\n 5 -->|output| 8;\n cf90b47e-652b-428e-8170-11929768a4d6[\"Output\\njbrowse_output\"];\n 8 --> cf90b47e-652b-428e-8170-11929768a4d6;\n style cf90b47e-652b-428e-8170-11929768a4d6 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"staramr\"];\n 0 -->|output| 3;\n 80c90033-b113-4ab0-aa74-bc854226af75[\"Output\\nstararm_detailed_summary\"];\n 3 --> 80c90033-b113-4ab0-aa74-bc854226af75;\n style 80c90033-b113-4ab0-aa74-bc854226af75 stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n 136fe6f9-5bed-4cfa-a226-93d7b18553a2[\"Output\\nbakta_annotation_summary\"];\n 4 --> 136fe6f9-5bed-4cfa-a226-93d7b18553a2;\n style 136fe6f9-5bed-4cfa-a226-93d7b18553a2 stroke:#2c3143,stroke-width:4px;\n 5[\"Bowtie2\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n f33376ae-d468-46b6-8c9f-681067c2051e[\"Output\\nbowtie_mapping_stats\"];\n 5 --> f33376ae-d468-46b6-8c9f-681067c2051e;\n style f33376ae-d468-46b6-8c9f-681067c2051e stroke:#2c3143,stroke-width:4px;\n 6[\"Select\"];\n 3 -->|detailed_summary| 6;\n 7[\"Table to GFF3\"];\n 6 -->|out_file1| 7;\n 8[\"JBrowse\"];\n 4 -->|annotation_gff3| 8;\n 7 -->|output| 8;\n 5 -->|output| 8;\n 20eae676-6d39-4ec3-a83d-ab27abd3ab91[\"Output\\njbrowse_output\"];\n 8 --> 20eae676-6d39-4ec3-a83d-ab27abd3ab91;\n style 20eae676-6d39-4ec3-a83d-ab27abd3ab91 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "mrsa AMR gene detection",
"outputs": [
{
@@ -341706,7 +308576,7 @@
{
"label": "stararm_detailed_summary",
"output_name": "detailed_summary",
- "uuid": "2f01e653-531f-44fe-85a7-b699a47ab683"
+ "uuid": "80c90033-b113-4ab0-aa74-bc854226af75"
}
]
},
@@ -341780,7 +308650,7 @@
{
"label": "bakta_annotation_summary",
"output_name": "annotation_tsv",
- "uuid": "4a680ee0-78c4-4733-b9f0-cb1a0ebcb174"
+ "uuid": "136fe6f9-5bed-4cfa-a226-93d7b18553a2"
}
]
},
@@ -341837,7 +308707,7 @@
{
"label": "bowtie_mapping_stats",
"output_name": "mapping_stats",
- "uuid": "a3c861ca-77bf-4118-8f3e-c452427aac79"
+ "uuid": "f33376ae-d468-46b6-8c9f-681067c2051e"
}
]
},
@@ -341890,7 +308760,7 @@
{
"label": "jbrowse_output",
"output_name": "output",
- "uuid": "cf90b47e-652b-428e-8170-11929768a4d6"
+ "uuid": "20eae676-6d39-4ec3-a83d-ab27abd3ab91"
}
]
}
@@ -342301,15 +309171,15 @@
"topic_0798"
],
"edam_operation": [
- "Sequence motif recognition",
- "Nucleic acid feature detection",
"Structural variation detection",
+ "Protein feature detection",
"Genome assembly",
"Genome annotation",
- "Protein feature detection",
- "Genome visualisation",
+ "Sequence motif recognition",
"Scaffolding",
- "Multilocus sequence typing"
+ "Nucleic acid feature detection",
+ "Multilocus sequence typing",
+ "Genome visualisation"
],
"edam_topic": [
"Genomics",
@@ -342321,8 +309191,7 @@
"Mobile genetic elements"
],
"exact_supported_servers": [
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -342375,7 +309244,7 @@
"Process the outputs to formate them for visualization needs",
"Visualize a draft bacterial genome and its annotations"
],
- "pageviews": 4233,
+ "pageviews": 4366,
"pub_date": "2024-02-01",
"questions": [
"Which genes are on a draft bacterial genome?",
@@ -342398,16 +309267,16 @@
],
"short_id": "T00403",
"short_tools": [
- "bakta",
"tp_replace_in_column",
+ "plasmidfinder",
+ "tp_tail_tool",
+ "Grouping1",
"isescan",
- "jbrowse",
"tbl2gff3",
- "plasmidfinder",
"integron_finder",
"upload1",
- "Grouping1",
- "tp_tail_tool"
+ "jbrowse",
+ "bakta"
],
"slides": false,
"slides_recordings": false,
@@ -342418,11 +309287,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -342465,6 +309329,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -342520,10 +309388,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -342570,11 +309434,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -342619,6 +309478,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -342671,10 +309534,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -342715,10 +309574,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -342761,6 +309616,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -342819,10 +309678,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -342876,11 +309731,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -342931,6 +309781,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -342989,10 +309843,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -343042,11 +309892,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -343094,6 +309939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343119,8 +309968,8 @@
"state": "inexact",
"versions": [
"1.8.1+galaxy1",
- "1.9.2+galaxy0",
- "1.8.2+galaxy0"
+ "1.8.2+galaxy0",
+ "1.9.2+galaxy0"
]
},
{
@@ -343151,10 +310000,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -343200,11 +310045,6 @@
"state": "exact",
"version": "1.9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -343223,10 +310063,10 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.2+galaxy0",
"1.8.2+galaxy0",
- "1.9.4+galaxy0",
- "1.5.0+galaxy0"
+ "1.9.2+galaxy0",
+ "1.5.0+galaxy0",
+ "1.9.4+galaxy0"
]
},
{
@@ -343259,6 +310099,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343317,10 +310161,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -343365,11 +310205,6 @@
"state": "exact",
"version": "2.0.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -343414,6 +310249,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343472,10 +310311,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -343520,11 +310355,6 @@
"state": "exact",
"version": "1.7.2.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7.2.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -343569,6 +310399,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343624,10 +310458,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -343663,23 +310493,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -343692,11 +310522,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -343742,6 +310567,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343795,10 +310624,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -343841,11 +310666,6 @@
"state": "exact",
"version": "2.1.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.6+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -343890,6 +310710,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -343943,10 +310767,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -343989,11 +310809,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -344038,6 +310853,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -344090,10 +310909,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -344134,10 +310949,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -344200,8 +311011,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 162,
- "visitors": 3101,
+ "visit_duration": 163,
+ "visitors": 3187,
"workflows": [
{
"creators": [
@@ -344271,7 +311082,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"ISEScan\"];\n 0 -->|output| 1;\n 2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n 1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n 2[\"PlasmidFinder\"];\n 0 -->|output| 2;\n 614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n 2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n 3[\"Integron Finder\"];\n 0 -->|output| 3;\n d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n 3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n 4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n 5[\"Group\"];\n 1 -->|all_results| 5;\n 6[\"Group\"];\n 1 -->|all_results| 6;\n 7[\"Replace Text\"];\n 2 -->|result_file| 7;\n 8[\"Select last\"];\n 7 -->|outfile| 8;\n 9[\"Table to GFF3\"];\n 8 -->|outfile| 9;\n 10[\"JBrowse\"];\n 0 -->|output| 10;\n 4 -->|annotation_gff3| 10;\n 9 -->|output| 10;\n 1 -->|annotation| 10;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Bacterial Genome Annotation",
"outputs": [
{
@@ -344849,7 +311660,6 @@
"Galaxy@AuBi",
"UseGalaxy.be",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -344881,7 +311691,7 @@
"Build several visualisations in JBrowse",
"Have basic familiarity with moving around JBrowse, and loading several data tracks"
],
- "pageviews": 6184631,
+ "pageviews": 6207648,
"pub_date": "2020-01-10",
"questions": [
"How can I visualise features or blast data?",
@@ -344910,11 +311720,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -344976,6 +311781,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -345031,10 +311840,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -345081,11 +311886,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -345130,6 +311930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -345190,10 +311994,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -345242,11 +312042,6 @@
"state": "exact",
"version": "1.16.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -345300,8 +312095,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 289,
- "visitors": 2246594,
+ "visit_duration": 290,
+ "visitors": 2257452,
"zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
},
{
@@ -345558,19 +312353,18 @@
],
"dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
"edam_operation": [
+ "Sequence alignment",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
"Sequence composition calculation",
- "Read mapping",
"Generation",
+ "Read mapping",
"Genome visualisation",
"Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -345604,7 +312398,7 @@
"Critique large data sets and use bioinformatics to assess genetics data",
"Tap into the interdisciplinary nature of science"
],
- "pageviews": 1042,
+ "pageviews": 1050,
"pub_date": "2023-07-10",
"questions": [
"How do I check my data quality?",
@@ -345613,8 +312407,8 @@
],
"short_id": "T00356",
"short_tools": [
- "jbrowse",
"fastqc",
+ "jbrowse",
"bwa_mem"
],
"slides": false,
@@ -345626,11 +312420,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -345702,6 +312491,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -345757,10 +312550,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -345807,11 +312596,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -345856,6 +312640,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -345915,10 +312703,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -345966,11 +312750,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -346017,6 +312796,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -346074,10 +312857,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -346103,8 +312882,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -346128,12 +312907,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -346143,9 +312922,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -346156,11 +312935,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -346206,6 +312980,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -346266,10 +313044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -346318,11 +313092,6 @@
"state": "exact",
"version": "1.16.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -346379,8 +313148,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 255,
- "visitors": 808,
+ "visit_duration": 256,
+ "visitors": 815,
"zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
},
{
@@ -346601,7 +313370,7 @@
"objectives": [
"Validate your genes and create an official gene set from them."
],
- "pageviews": 19,
+ "pageviews": 21,
"pub_date": "2023-11-02",
"questions": [
"I have several genomes assemblies that are not annotated (or I do not trust annotations)",
@@ -346677,8 +313446,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 4,
- "visitors": 16,
+ "visit_duration": 5,
+ "visitors": 18,
"zenodo_link": ""
},
{
@@ -347225,26 +313994,25 @@
],
"dir": "topics/genome-annotation/tutorials/funannotate",
"edam_operation": [
- "Sequence motif recognition",
- "Genome visualisation",
- "Formatting",
- "Genome assembly",
- "Sequence annotation",
"Fold recognition",
- "Information extraction",
- "Sequence alignment",
- "Sequence assembly validation",
"Homology-based gene prediction",
+ "Information extraction",
+ "Genome assembly",
"Genome annotation",
+ "Sequence assembly validation",
+ "Sequence annotation",
+ "Sequence motif recognition",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Formatting",
"Protein feature detection",
"Query and retrieval",
- "Transcriptome assembly",
- "Scaffolding"
+ "Sequence alignment",
+ "Genome visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -347286,7 +314054,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 11690,
+ "pageviews": 11741,
"priority": 2,
"pub_date": "2021-11-29",
"questions": [
@@ -347332,15 +314100,15 @@
],
"short_id": "T00172",
"short_tools": [
- "eggnog_mapper",
- "picard_MergeSamFiles",
- "busco",
- "jbrowse",
"funannotate_predict",
- "interproscan",
- "funannotate_compare",
"funannotate_annotate",
+ "jbrowse",
+ "busco",
"rna_star",
+ "funannotate_compare",
+ "interproscan",
+ "eggnog_mapper",
+ "picard_MergeSamFiles",
"aegean_parseval"
],
"slides": false,
@@ -347353,11 +314121,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -347404,6 +314167,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -347459,10 +314226,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -347509,11 +314272,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -347558,6 +314316,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -347610,10 +314372,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -347646,8 +314404,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "5.52-86.0+galaxy1",
- "5.54-87.0+galaxy2"
+ "5.54-87.0+galaxy2",
+ "5.52-86.0+galaxy1"
]
},
{
@@ -347660,11 +314418,6 @@
"state": "exact",
"version": "5.59-91.0+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.59-91.0+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -347710,6 +314463,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -347764,10 +314521,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -347814,11 +314567,6 @@
"state": "exact",
"version": "2.18.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -347864,6 +314612,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -347916,10 +314668,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -347969,11 +314717,6 @@
"state": "exact",
"version": "2.1.8+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.8+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -348022,6 +314765,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348074,10 +314821,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348121,11 +314864,6 @@
"state": "exact",
"version": "0.16.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.16.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -348170,6 +314908,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348223,10 +314965,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348272,23 +315010,18 @@
"state": "exact",
"version": "5.4.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.4.6+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -348331,6 +315064,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348383,10 +315120,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348434,11 +315167,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -348454,10 +315182,10 @@
"versions": [
"1.8.9+galaxy2",
"1.8.15+galaxy5",
- "1.8.15+galaxy3",
- "1.8.15+galaxy1",
- "1.8.15+galaxy4",
"1.8.9+galaxy3",
+ "1.8.15+galaxy4",
+ "1.8.15+galaxy1",
+ "1.8.15+galaxy3",
"1.8.15+galaxy2"
]
},
@@ -348491,6 +315219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348543,10 +315275,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348594,11 +315322,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -348643,6 +315366,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348695,10 +315422,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348746,11 +315469,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -348767,10 +315485,10 @@
"1.8.9+galaxy2",
"1.8.15+galaxy5",
"1.8.15+galaxy1",
- "1.8.15+galaxy4",
"1.8.15+galaxy2",
"1.8.9+galaxy3",
- "1.8.15+galaxy3"
+ "1.8.15+galaxy3",
+ "1.8.15+galaxy4"
]
},
{
@@ -348803,6 +315521,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -348855,10 +315577,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -348906,11 +315624,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -348955,6 +315668,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -349007,10 +315724,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -349059,11 +315772,6 @@
"state": "exact",
"version": "1.8.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -349079,11 +315787,11 @@
"versions": [
"1.8.15+galaxy5",
"1.8.9+galaxy2",
- "1.8.9+galaxy3",
- "1.8.15+galaxy2",
- "1.8.15+galaxy1",
+ "1.8.15+galaxy3",
"1.8.15+galaxy4",
- "1.8.15+galaxy3"
+ "1.8.15+galaxy1",
+ "1.8.15+galaxy2",
+ "1.8.9+galaxy3"
]
},
{
@@ -349116,6 +315824,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -349168,10 +315880,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -349220,11 +315928,6 @@
"state": "exact",
"version": "1.8.15+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.15+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -349269,6 +315972,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -349324,10 +316031,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -349363,23 +316066,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -349392,11 +316095,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -349442,6 +316140,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -349467,8 +316169,8 @@
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -349505,10 +316207,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -349547,16 +316245,16 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
@@ -349569,11 +316267,6 @@
"state": "exact",
"version": "2.7.10b+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.10b+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -349626,6 +316319,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -349685,10 +316382,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -349727,24 +316420,24 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -349752,11 +316445,6 @@
"state": "exact",
"version": "2.7.8a+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.8a+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -349825,7 +316513,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 125,
- "visitors": 7847,
+ "visitors": 7893,
"workflows": [
{
"creators": [
@@ -350038,7 +316726,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"RNA STAR\"];\n 0 -->|output| 7;\n 1 -->|output| 7;\n 2 -->|output| 7;\n 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n 7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n 8[\"Funannotate predict annotation\"];\n 3 -->|output| 8;\n 7 -->|mapped_reads| 8;\n 0 -->|output| 8;\n 9[\"eggNOG Mapper\"];\n 8 -->|fasta_proteins| 9;\n 10[\"InterProScan\"];\n 8 -->|fasta_proteins| 10;\n 11[\"Funannotate functional\"];\n 9 -->|annotations| 11;\n 8 -->|annot_gbk| 11;\n 10 -->|outfile_xml| 11;\n 4 -->|output| 11;\n d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n 11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n 9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n 11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n 99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n 11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n 17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n 11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n 4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n 11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n 12[\"JBrowse\"];\n 0 -->|output| 12;\n 11 -->|gff3| 12;\n 7 -->|mapped_reads| 12;\n ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n 12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n 13[\"Funannotate compare\"];\n 5 -->|output| 13;\n 11 -->|gbk| 13;\n e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n 13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n 14[\"AEGeAn ParsEval\"];\n 6 -->|output| 14;\n 11 -->|gff3| 14;\n 0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n 14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n 15[\"Busco\"];\n 11 -->|fa_proteins| 15;\n 57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n 15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n 97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n 15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Funannotate",
"outputs": [
{
@@ -350980,17 +317668,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n owner: devteam\n revisions: 0232f19d300f\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 1440ae06552f\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions: 2bb2e07a7a21\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n owner: iuc\n revisions: 8cffbd184762\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n owner: iuc\n revisions: 96ac930d84fa\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n owner: iuc\n revisions: 326f9c294b09\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n owner: simon-gladman\n revisions: 20ca2574216a\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
- "contributions": {
- "authorship": [
- "abretaud"
- ],
- "reviewing": [
- "bgruening",
- "bebatut",
- "abretaud",
- "hexylena"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -351016,128 +317693,17 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
"twitter": "abretau",
"url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
"edam_operation": [
+ "Transcriptome assembly",
+ "Genome assembly",
"Genome annotation",
"Sequence assembly validation",
- "Genome assembly",
"Sequence annotation",
"Genome visualisation",
- "Scaffolding",
- "Transcriptome assembly"
+ "Scaffolding"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -351166,7 +317732,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 4428,
+ "pageviews": 4550,
"priority": 3,
"pub_date": "2021-01-12",
"questions": [
@@ -351175,13 +317741,13 @@
],
"short_id": "T00167",
"short_tools": [
+ "maker",
+ "jcvi_gff_stats",
+ "maker_map_ids",
"fasta-stats",
"gffread",
"jbrowse",
- "jcvi_gff_stats",
- "maker_map_ids",
- "busco",
- "maker"
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -351218,6 +317784,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -351273,10 +317843,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -351323,11 +317889,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -351372,6 +317933,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -351427,10 +317992,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -351476,14 +318037,6 @@
"state": "exact",
"version": "2.2.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1.3+galaxy0",
- "2.2.1.4+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -351498,8 +318051,8 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
"2.2.1.2",
+ "2.2.1.0",
"2.2.1.3+galaxy0",
"2.2.1.4+galaxy0"
]
@@ -351543,6 +318096,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -351575,10 +318132,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -351601,10 +318158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -351652,53 +318205,36 @@
"state": "exact",
"version": "3.0.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
- "5.2.2+galaxy2",
- "5.3.1+galaxy0",
- "5.3.2+galaxy0",
- "5.5.0+galaxy0",
- "5.2.2+galaxy0",
- "5.7.1+galaxy0",
- "5.8.0+galaxy0",
- "5.4.5+galaxy0",
- "5.2.2+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "5.4.6+galaxy0",
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
+ "5.4.6+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "3.0.2+galaxy2",
- "4.1.2",
"5.3.2+galaxy0",
"5.5.0+galaxy0",
- "5.2.2+galaxy0",
+ "3.0.2+galaxy2",
+ "5.8.0+galaxy0",
"5.7.1+galaxy0",
- "5.8.0+galaxy0"
+ "4.1.2",
+ "5.2.2+galaxy0"
]
},
{
@@ -351736,6 +318272,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -351799,10 +318339,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -351851,17 +318387,6 @@
"state": "exact",
"version": "1.16.4+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.16.9+galaxy0",
- "1.16.11+galaxy1",
- "1.16.10+galaxy0",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -351911,6 +318436,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -351963,10 +318492,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -352010,11 +318535,6 @@
"state": "exact",
"version": "0.8.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -352060,6 +318580,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -352092,8 +318616,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.31.11",
- "2.31.10+galaxy1"
+ "2.31.10+galaxy1",
+ "2.31.11"
]
},
{
@@ -352116,10 +318640,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -352168,20 +318688,12 @@
"state": "exact",
"version": "2.31.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11+galaxy1",
- "2.31.11+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.31.11",
"2.31.10+galaxy1",
+ "2.31.11",
"2.31.11+galaxy1",
"2.31.11+galaxy2"
]
@@ -352190,8 +318702,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "2.31.11",
"2.31.10+galaxy1",
+ "2.31.11",
"2.31.11+galaxy1",
"2.31.11+galaxy2"
]
@@ -352235,6 +318747,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -352287,10 +318803,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -352338,13 +318850,6 @@
"state": "exact",
"version": "2.31.10"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -352390,6 +318895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -352443,10 +318952,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -352488,10 +318993,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -352550,8 +319051,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 194,
- "visitors": 3050,
+ "visit_duration": 192,
+ "visitors": 3138,
"workflows": [
{
"creators": [],
@@ -352773,7 +319274,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Fasta Statistics\"];\n 0 -->|output| 5;\n 6[\"Busco\"];\n 0 -->|output| 6;\n 7[\"Maker\"];\n 4 -->|output| 7;\n 3 -->|output| 7;\n 1 -->|output| 7;\n 0 -->|output| 7;\n 2 -->|output| 7;\n 8[\"Map annotation ids\"];\n 7 -->|output_gff| 8;\n 9[\"Genome annotation statistics\"];\n 8 -->|renamed| 9;\n 0 -->|output| 9;\n 10[\"gffread\"];\n 8 -->|renamed| 10;\n 0 -->|output| 10;\n 11[\"JBrowse\"];\n 0 -->|output| 11;\n 8 -->|renamed| 11;\n 7 -->|output_evidences| 11;\n 12[\"Busco\"];\n 10 -->|output_exons| 12;\n 6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n 12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome annotation with Maker (short)",
"outputs": [
{
@@ -353528,20 +320029,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: augustus_training\n owner: bgruening\n revisions: 6519ebe25019\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n owner: devteam\n revisions: 69e0806b63a4\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 602fb8e63aa7\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n owner: iuc\n revisions: 9c620a950d3a\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions: 6cd09d7b5f37\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n owner: iuc\n revisions: 8cffbd184762\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n owner: iuc\n revisions: d46d803ca6cc\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n owner: iuc\n revisions: e906fa778440\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snap_training\n owner: iuc\n revisions: 2a598c0aa042\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "reviewing": [
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- "shiltemann",
- "bebatut",
- "abretaud",
- "nsoranzo",
- "hexylena",
- "lecorguille"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -353567,194 +320054,21 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
"twitter": "abretau",
"url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
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- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
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- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
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- "linkedin": "shiltemann",
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- "lon": 4.462
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
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- "ifb",
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
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- "linkedin": "berenicebatut",
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- "eurosciencegateway",
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
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- "location": {
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- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
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- "twitter": "abretau",
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- "fediverse": "https://mstdn.science/@nsoranzo",
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- "joined": "2017-09",
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- "matrix": "nsoranzo:matrix.org",
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- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "elixir-europe",
- "elixir-converge"
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- "former_affiliations": [
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- "uni-freiburg"
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- "id": "hexylena",
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- "lon": 4.46
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- "maintainer_contact": "gitter",
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- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/genome-annotation/tutorials/annotation-with-maker",
"edam_operation": [
- "Operation",
- "Genome assembly",
- "Sequence annotation",
- "Sequence assembly validation",
"Homology-based gene prediction",
+ "Genome assembly",
"Genome annotation",
+ "Sequence assembly validation",
+ "Sequence annotation",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Operation",
"Gene prediction",
"Ab-initio gene prediction",
- "Genome visualisation",
- "Scaffolding",
- "Transcriptome assembly"
+ "Genome visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -353789,7 +320103,7 @@
"Evaluate annotation quality with BUSCO",
"View annotations in JBrowse"
],
- "pageviews": 22324,
+ "pageviews": 22451,
"priority": 4,
"pub_date": "2018-09-24",
"questions": [
@@ -353800,13 +320114,13 @@
"short_tools": [
"augustus_training",
"snap_training",
+ "maker",
+ "jcvi_gff_stats",
+ "maker_map_ids",
"fasta-stats",
"gffread",
"jbrowse",
- "jcvi_gff_stats",
- "maker_map_ids",
- "busco",
- "maker"
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -353869,6 +320183,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -353924,10 +320242,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -353974,11 +320288,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -354023,6 +320332,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -354076,10 +320389,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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"state": "missing"
@@ -354125,14 +320434,6 @@
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- "3.4.0+galaxy2"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -354178,6 +320479,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -354233,174 +320538,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
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@@ -354432,37 +320569,176 @@
{
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- "version": "4.1.4"
+ "version": "2.2.1.2"
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{
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+ "2.2.1.3+galaxy0"
]
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{
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"state": "exact",
- "version": "4.1.4"
+ "version": "2.2.1.2"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2.2.1.2"
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+ "state": "exact",
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+ "state": "inexact",
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+ "2.2.1.3+galaxy0",
+ "2.2.1.4+galaxy0"
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- "5.7.1+galaxy0",
- "5.8.0+galaxy0",
- "5.4.5+galaxy0",
- "5.2.2+galaxy1"
+ "5.0.0+galaxy0",
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "4.1.4"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "5.4.6+galaxy0"
]
},
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "4.1.4"
+ },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -354508,6 +320784,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -354565,10 +320845,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -354614,14 +320890,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0",
- "1.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -354667,6 +320935,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -354727,10 +320999,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -354779,11 +321047,6 @@
"state": "exact",
"version": "1.16.10+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.10+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -354829,6 +321092,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -354881,10 +321148,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -354928,11 +321191,6 @@
"state": "exact",
"version": "0.8.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -354978,6 +321236,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -355031,10 +321293,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -355080,14 +321338,6 @@
"state": "exact",
"version": "2.31.11"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.31.11+galaxy1",
- "2.31.11+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -355133,6 +321383,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -355185,10 +321439,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -355232,11 +321482,6 @@
"state": "exact",
"version": "2.31.11"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.31.11"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -355282,6 +321527,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -355334,10 +321583,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -355381,10 +321626,6 @@
"state": "exact",
"version": "2013_11_29+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -355449,7 +321690,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 113,
- "visitors": 12168,
+ "visitors": 12246,
"workflows": [
{
"creators": [
@@ -355657,7 +321898,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Maker\"];\n 0 -->|output| 3;\n 2 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Fasta Statistics\"];\n 2 -->|output| 4;\n 2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n 4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n 5[\"Busco\"];\n 2 -->|output| 5;\n a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n 5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n 7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n 5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n 5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n 6[\"Train Augustus\"];\n 2 -->|output| 6;\n 3 -->|output_gff| 6;\n 7[\"Genome annotation statistics\"];\n 3 -->|output_gff| 7;\n 2 -->|output| 7;\n 2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n 7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n 71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n 7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n 8[\"gffread\"];\n 3 -->|output_gff| 8;\n 2 -->|output| 8;\n 9[\"Train SNAP\"];\n 2 -->|output| 9;\n 3 -->|output_gff| 9;\n 10[\"Busco\"];\n 8 -->|output_exons| 10;\n a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n 10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n 11[\"Maker\"];\n 6 -->|output_tar| 11;\n 9 -->|output| 11;\n 2 -->|output| 11;\n 3 -->|output_full| 11;\n 12[\"gffread\"];\n 11 -->|output_gff| 12;\n 2 -->|output| 12;\n 13[\"Train Augustus\"];\n 2 -->|output| 13;\n 11 -->|output_gff| 13;\n 42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n 13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n 14[\"Genome annotation statistics\"];\n 11 -->|output_gff| 14;\n 2 -->|output| 14;\n 9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n 14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n 61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n 14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n 15[\"Train SNAP\"];\n 2 -->|output| 15;\n 11 -->|output_gff| 15;\n 458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n 15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n 16[\"Busco\"];\n 12 -->|output_exons| 16;\n f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n 16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n 17[\"Maker\"];\n 13 -->|output_tar| 17;\n 15 -->|output| 17;\n 2 -->|output| 17;\n 11 -->|output_full| 17;\n 18[\"Map annotation ids\"];\n 17 -->|output_gff| 18;\n 63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n 18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n 19[\"JBrowse\"];\n 2 -->|output| 19;\n 3 -->|output_gff| 19;\n 18 -->|renamed| 19;\n 11 -->|output_gff| 19;\n 3 -->|output_evidences| 19;\n 11 -->|output_evidences| 19;\n 17 -->|output_evidences| 19;\n 5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n 19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n 20[\"gffread\"];\n 18 -->|renamed| 20;\n 2 -->|output| 20;\n 52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n 20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n 5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n 20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n 84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n 20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n 21[\"Genome annotation statistics\"];\n 18 -->|renamed| 21;\n 2 -->|output| 21;\n f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n 21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n 21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n 22[\"Busco\"];\n 20 -->|output_exons| 22;\n 0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n 22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Genome annotation with Maker ",
"outputs": [
{
@@ -356856,7 +323097,7 @@
"Learn how to manually refine genome annotations within Apollo",
"Export refined genome annotations"
],
- "pageviews": 1667,
+ "pageviews": 1671,
"priority": 6,
"pub_date": "2022-08-22",
"questions": [
@@ -356883,9 +323124,9 @@
],
"short_id": "T00170",
"short_tools": [
- "iframe",
+ "jbrowse",
"create_or_update",
- "jbrowse"
+ "iframe"
],
"slides": false,
"slides_recordings": false,
@@ -356933,6 +323174,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -356988,10 +323233,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -357038,11 +323279,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -357087,6 +323323,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -357139,10 +323379,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -357189,10 +323425,6 @@
"4.2.13+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -357236,6 +323468,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -357288,10 +323524,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -357336,10 +323568,6 @@
"state": "exact",
"version": "4.2.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -357383,6 +323611,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -357438,10 +323670,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -357477,23 +323705,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -357506,11 +323734,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -357570,7 +323793,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 155,
- "visitors": 981,
+ "visitors": 985,
"zenodo_link": "https://zenodo.org/record/3270822"
},
{
@@ -357633,7 +323856,8 @@
"bgruening"
],
"funding": [
- "nfdi4bioimage"
+ "nfdi4bioimage",
+ "dfg"
],
"reviewing": [
"bgruening",
@@ -357686,15 +323910,29 @@
},
{
"avatar": "/training-material/shared/images/nfdi4bioimage.jpeg",
+ "funder_name": "DFG",
+ "funding_database": "dfg",
+ "funding_id": "501864659",
+ "github": false,
"id": "nfdi4bioimage",
- "joined": "2024-11",
+ "joined": "2024-12",
"members": [
"rmassei"
],
- "name": "NFDI4BIOIMAGE",
+ "name": "NFDI4Bioimage",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4bioimage/",
- "short_name": "NFDI4BIOIMAGE",
- "url": "https://training.galaxyproject.org/training-material/api/organisations/nfdi4bioimage.json"
+ "short_name": "NFDI4Bioimage",
+ "url": "https://training.galaxyproject.org/training-material/api/grants/nfdi4bioimage.json"
+ },
+ {
+ "avatar": "/training-material/shared/images/DFG_grant.png",
+ "github": false,
+ "id": "dfg",
+ "joined": "2024-12",
+ "name": "Deutsche Forschungsgemeinschaft",
+ "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dfg/",
+ "short_name": "DFG",
+ "url": "https://training.galaxyproject.org/training-material/api/organisations/dfg.json"
},
{
"affiliations": [
@@ -357763,12 +324001,12 @@
"layout": "tutorial_hands_on",
"level": "Intermediate",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-04",
+ "mod_date": "2024-12-11",
"objectives": [
"Understand how the different tools of the Galaxy OMERO-suite works",
"Build a complete pipeline for image and metadata upload into OMERO"
],
- "pageviews": 15,
+ "pageviews": 19,
"pub_date": "2024-12-04",
"questions": [
"How can I use Galaxy to upload images and metadata into OMERO?",
@@ -357776,11 +324014,11 @@
],
"short_id": "T00477",
"short_tools": [
- "omero_import",
"omero_filter",
- "omero_get_value",
- "omero_roi_import",
"omero_metadata_import",
+ "omero_roi_import",
+ "omero_import",
+ "omero_get_value",
"omero_get_id"
],
"slides": false,
@@ -357811,6 +324049,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -357866,10 +324108,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -357916,11 +324154,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -357965,6 +324198,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358017,10 +324254,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358061,10 +324294,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358107,6 +324336,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358159,10 +324392,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358203,10 +324432,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358249,6 +324474,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358301,10 +324530,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358345,10 +324570,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358391,6 +324612,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358443,10 +324668,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358487,10 +324708,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358533,6 +324750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358585,10 +324806,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358629,10 +324846,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358675,6 +324888,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -358727,10 +324944,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -358771,10 +324984,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -358822,12 +325031,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/omero-suite/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/omero-suite/tutorial.json"
},
- "version": 1,
+ "version": 2,
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 140,
- "visitors": 7,
+ "visit_duration": 142,
+ "visitors": 10,
"zenodo_link": "https://zenodo.org/records/14205500"
},
{
@@ -359085,7 +325294,7 @@
"Segment fluorescent objects using CellProfiler in Galaxy",
"Track objects over multiple frames using CellProfiler in Galaxy"
],
- "pageviews": 2398,
+ "pageviews": 2401,
"pub_date": "2021-03-17",
"questions": [
"How to segment and track objects in fluorescence time-lapse microscopy images?"
@@ -359101,17 +325310,17 @@
],
"short_id": "T00182",
"short_tools": [
- "cp_track_objects",
- "cp_export_to_spreadsheet",
+ "cp_overlay_outlines",
+ "cp_identify_primary_objects",
"cp_color_to_gray",
+ "cp_common",
+ "cp_export_to_spreadsheet",
"unzip",
- "cp_save_images",
+ "cp_track_objects",
"cp_tile",
"cp_measure_object_intensity",
+ "cp_save_images",
"cp_measure_object_size_shape",
- "cp_overlay_outlines",
- "cp_common",
- "cp_identify_primary_objects",
"cp_cellprofiler"
],
"slides": false,
@@ -359159,6 +325368,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -359214,10 +325427,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -359264,11 +325473,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -359313,6 +325517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -359365,10 +325573,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -359414,13 +325618,6 @@
"state": "exact",
"version": "3.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -359465,6 +325662,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -359517,10 +325718,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -359563,10 +325760,6 @@
"state": "exact",
"version": "3.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -359610,6 +325803,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -359662,10 +325859,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -359711,13 +325904,6 @@
"state": "exact",
"version": "3.1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -359762,6 +325948,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -359814,10 +326004,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -359863,13 +326049,6 @@
"state": "exact",
"version": "3.1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -359914,6 +326093,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -359966,10 +326149,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -360015,13 +326194,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -360066,6 +326238,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360118,10 +326294,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
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"state": "missing"
@@ -360167,13 +326339,6 @@
"state": "exact",
"version": "3.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -360218,6 +326383,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360270,10 +326439,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -360319,13 +326484,6 @@
"state": "exact",
"version": "3.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -360370,6 +326528,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360422,10 +326584,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -360468,10 +326626,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -360515,6 +326669,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360567,10 +326725,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -360616,13 +326770,6 @@
"state": "exact",
"version": "3.1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -360667,6 +326814,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360719,10 +326870,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
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"state": "missing"
@@ -360765,10 +326912,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
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"state": "missing"
@@ -360812,6 +326955,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -360864,10 +327011,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
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"state": "missing"
@@ -360910,10 +327053,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
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"state": "missing"
@@ -360957,6 +327096,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -361010,10 +327153,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -361059,13 +327198,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "6.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -361126,7 +327258,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 62,
- "visitors": 1909,
+ "visitors": 1912,
"workflows": [
{
"creators": [],
@@ -361205,7 +327337,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"Starting Modules\"];\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"ColorToGray\"];\n 0 -->|output_pipeline| 2;\n 3[\"Unzip\"];\n 1 -->|output| 3;\n 4[\"IdentifyPrimaryObjects\"];\n 2 -->|output_pipeline| 4;\n 5[\"MeasureObjectSizeShape\"];\n 4 -->|output_pipeline| 5;\n 6[\"MeasureObjectIntensity\"];\n 5 -->|output_pipeline| 6;\n 7[\"TrackObjects\"];\n 6 -->|output_pipeline| 7;\n 8[\"OverlayOutlines\"];\n 7 -->|output_pipeline| 8;\n 9[\"Tile\"];\n 8 -->|output_pipeline| 9;\n 10[\"SaveImages\"];\n 9 -->|output_pipeline| 10;\n 11[\"ExportToSpreadsheet\"];\n 10 -->|output_pipeline| 11;\n 12[\"CellProfiler\"];\n 3 -->|unzipped| 12;\n 11 -->|output_pipeline| 12;\n dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e[\"Output\\nCellProfiler pipeline output files\"];\n 12 --> dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e;\n style dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "CP_object_tracking_example",
"outputs": [
{
@@ -362254,10 +328386,10 @@
],
"dir": "topics/imaging/tutorials/imaging-introduction",
"edam_operation": [
- "Image analysis",
- "Visualisation",
+ "Image annotation",
"Data handling",
- "Image annotation"
+ "Image analysis",
+ "Visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -362297,7 +328429,7 @@
"How to handle images in Galaxy.",
"How to perform basic image processing in Galaxy."
],
- "pageviews": 3046,
+ "pageviews": 3048,
"pub_date": "2019-08-13",
"questions": [
"How do I use Galaxy with imaging data?",
@@ -362308,13 +328440,13 @@
],
"short_id": "T00181",
"short_tools": [
+ "ip_filter_standard",
"ip_threshold",
- "ip_histogram_equalization",
- "unzip",
- "ip_overlay_images",
"ip_count_objects",
+ "unzip",
+ "ip_histogram_equalization",
"ip_binary_to_labelimage",
- "ip_filter_standard",
+ "ip_overlay_images",
"ip_imageinfo"
],
"slides": false,
@@ -362362,6 +328494,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -362417,10 +328553,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -362467,11 +328599,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -362516,6 +328643,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -362568,10 +328699,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -362604,8 +328731,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.0.4",
- "0.0.3"
+ "0.0.3",
+ "0.0.4"
]
},
{
@@ -362621,11 +328748,6 @@
"state": "exact",
"version": "0.18.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.18.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -362673,6 +328795,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -362725,10 +328851,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -362776,11 +328898,6 @@
"state": "exact",
"version": "0.18.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.18.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -362828,6 +328945,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -362880,10 +329001,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -362932,11 +329049,6 @@
"state": "exact",
"version": "1.12.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.12.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -362984,6 +329096,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -363036,10 +329152,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -363087,10 +329199,6 @@
"state": "exact",
"version": "0.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -363138,6 +329246,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -363190,10 +329302,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -363242,11 +329350,6 @@
"state": "exact",
"version": "0.0.5-2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.5-2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -363294,6 +329397,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -363346,10 +329453,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -363397,11 +329500,6 @@
"state": "exact",
"version": "5.7.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.7.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -363448,6 +329546,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -363500,10 +329602,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -363540,9 +329638,9 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.0.3",
"0.0.2",
- "0.0.1"
+ "0.0.1",
+ "0.0.3"
]
},
{
@@ -363550,11 +329648,6 @@
"state": "exact",
"version": "0.0.4+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.4+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -363599,6 +329692,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -363654,10 +329751,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -363703,11 +329796,6 @@
"state": "exact",
"version": "6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -363769,7 +329857,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 97,
- "visitors": 2113,
+ "visitors": 2115,
"workflows": [
{
"creators": [
@@ -363904,7 +329992,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ninput_image\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Show image info\"];\n 0 -->|output| 1;\n 2[\"Filter 2-D image\"];\n 0 -->|output| 2;\n 3[\"Perform histogram equalization\"];\n 2 -->|output| 3;\n 4[\"Threshold image\"];\n 2 -->|output| 4;\n 5[\"Convert binary image to label map\"];\n 4 -->|output| 5;\n 6[\"Overlay images\"];\n 3 -->|output| 6;\n 5 -->|output| 6;\n d362c206-756d-4f04-82f0-bd6f24907e04[\"Output\\nout_png\"];\n 6 --> d362c206-756d-4f04-82f0-bd6f24907e04;\n style d362c206-756d-4f04-82f0-bd6f24907e04 stroke:#2c3143,stroke-width:4px;\n 7[\"Count objects in label map\"];\n 5 -->|output| 7;\n 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4[\"Output\\noutput\"];\n 7 --> 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4;\n style 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Workflow constructed from Tutorial 'Introduction to Image Analysis using Galaxy'",
"outputs": [
{
@@ -364229,7 +330317,7 @@
"Learn to track mitochondrial movements in live-cell imaging data.",
"Use image analysis tools to detect and quantify mitoflashes."
],
- "pageviews": 31,
+ "pageviews": 41,
"pub_date": "2024-11-20",
"questions": [
"What are mitoflashes, and why are they relevant for understanding mitochondrial function?",
@@ -364237,9 +330325,9 @@
],
"short_id": "T00472",
"short_tools": [
- "ip_spot_detection_2d",
"ip_points_association_nn",
- "ip_curve_fitting"
+ "ip_curve_fitting",
+ "ip_spot_detection_2d"
],
"slides": false,
"slides_recordings": false,
@@ -364281,6 +330369,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -364336,10 +330428,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -364386,11 +330474,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -364435,6 +330518,154 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "0.0.3",
+ "0.0.1",
+ "0.0.2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.0.3-2"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "missing"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.0.3-2"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn/0.0.3-2",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -364487,10 +330718,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -364527,8 +330754,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.0.2",
"0.0.3",
+ "0.0.2",
"0.0.1"
]
},
@@ -364537,10 +330764,6 @@
"state": "exact",
"version": "0.0.3-2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -364561,7 +330784,7 @@
"version": "0.0.3-2"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn/0.0.3-2",
+ "id": "toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.0.1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -364584,151 +330807,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
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- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "0.0.2",
- "0.0.3",
- "0.0.1"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.0.3-2"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "0.0.3-2"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.0.1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -364783,10 +330862,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -364829,10 +330904,6 @@
"state": "exact",
"version": "0.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -364886,8 +330957,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 13,
- "visitors": 20,
+ "visit_duration": 174,
+ "visitors": 27,
"workflows": [
{
"creators": [
@@ -364918,7 +330989,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Mitochondrion detection\"];\n b84bfb33-15eb-4984-b109-fab32f3813df[\"Output\\nSpot Detection of Mitoflashes\"];\n 0 --> b84bfb33-15eb-4984-b109-fab32f3813df;\n style b84bfb33-15eb-4984-b109-fab32f3813df stroke:#2c3143,stroke-width:4px;\n 1[\"Mitochondrion tracking\"];\n 0 -->|fn_out| 1;\n a25e8913-0019-4dd3-aed4-8138e7dd8da3[\"Output\\nSpot Detection Across Frames\"];\n 1 --> a25e8913-0019-4dd3-aed4-8138e7dd8da3;\n style a25e8913-0019-4dd3-aed4-8138e7dd8da3 stroke:#2c3143,stroke-width:4px;\n 2[\"Curve fitting to measured intensities\"];\n 1 -->|fn_out| 2;\n a978b043-f089-4d41-8f5d-0df99915dd45[\"Output\\nCurve Fitting for Mitoflash Detection\"];\n 2 --> a978b043-f089-4d41-8f5d-0df99915dd45;\n style a978b043-f089-4d41-8f5d-0df99915dd45 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Capturing mitoflashes",
"outputs": [
{
@@ -365295,7 +331366,7 @@
"Understand the tools available in Galaxy for multiplex tissue imaging analysis",
"Analyze and visualize publicly available TMA data using Galaxy"
],
- "pageviews": 1193,
+ "pageviews": 1206,
"pub_date": "2023-02-14",
"questions": [
"What tools are available for pre-processing multiplex tissue images in Galaxy?",
@@ -365306,16 +331377,16 @@
],
"short_id": "T00334",
"short_tools": [
- "mesmer",
"ip_convertimage",
- "ashlar",
"unet_coreograph",
"scimap_mcmicro_to_anndata",
- "vitessce_spatial",
+ "ashlar",
"basic_illumination",
- "quantification",
+ "rename_tiff_channels",
+ "mesmer",
"scimap_phenotyping",
- "rename_tiff_channels"
+ "quantification",
+ "vitessce_spatial"
],
"slides": false,
"slides_recordings": false,
@@ -365356,6 +331427,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -365411,10 +331486,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -365461,11 +331532,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -365510,6 +331576,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -365562,10 +331632,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -365611,10 +331677,6 @@
"state": "exact",
"version": "0.12.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -365660,6 +331722,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -365712,10 +331778,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -365759,10 +331821,6 @@
"state": "exact",
"version": "0.0.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -365806,6 +331864,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -365858,10 +331920,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -365903,10 +331961,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -365950,6 +332004,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366002,10 +332060,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366047,10 +332101,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -366094,6 +332144,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366146,10 +332200,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366193,10 +332243,6 @@
"state": "exact",
"version": "1.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -366246,6 +332292,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366298,10 +332348,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366334,8 +332380,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.4",
- "6.7.0+galaxy2"
+ "6.7.0+galaxy2",
+ "0.4"
]
},
{
@@ -366348,14 +332394,6 @@
"state": "exact",
"version": "6.7.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "6.7.0+galaxy2",
- "6.7.0+galaxy3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -366406,6 +332444,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366458,10 +332500,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366505,10 +332543,6 @@
"state": "exact",
"version": "1.14.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -366552,6 +332586,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366604,10 +332642,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366651,10 +332685,6 @@
"state": "exact",
"version": "1.0.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -366698,6 +332728,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366750,10 +332784,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366797,10 +332827,6 @@
"state": "exact",
"version": "2.2.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -366844,6 +332870,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -366896,10 +332926,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -366947,10 +332973,6 @@
"1.5.1+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -367011,8 +333033,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 112,
- "visitors": 864,
+ "visit_duration": 111,
+ "visitors": 877,
"workflows": [
{
"creators": [],
@@ -367147,7 +333169,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"BaSiC Illumination\"];\n 0 -->|output| 3;\n 4[\"ASHLAR\"];\n 3 -->|output_dfp| 4;\n 3 -->|output_ffp| 4;\n 0 -->|output| 4;\n 1 -->|output| 4;\n 5[\"UNetCoreograph\"];\n 4 -->|output| 5;\n 6[\"Mesmer\"];\n 5 -->|tma_sections| 6;\n ee73bee3-59e7-4e1c-87fd-197b8eac7e15[\"Output\\nMesmer on input dataset(s): Mask\"];\n 6 --> ee73bee3-59e7-4e1c-87fd-197b8eac7e15;\n style ee73bee3-59e7-4e1c-87fd-197b8eac7e15 stroke:#2c3143,stroke-width:4px;\n 7[\"Convert image\"];\n 5 -->|tma_sections| 7;\n 8[\"MCQUANT\"];\n 1 -->|output| 8;\n 5 -->|tma_sections| 8;\n 6 -->|mask| 8;\n fe28534a-2b3f-4ecc-8ba9-a106b2d1425c[\"Output\\nPrimary Mask Quantification\"];\n 8 --> fe28534a-2b3f-4ecc-8ba9-a106b2d1425c;\n style fe28534a-2b3f-4ecc-8ba9-a106b2d1425c stroke:#2c3143,stroke-width:4px;\n 9[\"Rename OME-TIFF Channels\"];\n 1 -->|output| 9;\n 7 -->|output| 9;\n 10[\"Convert McMicro Output to Anndata\"];\n 8 -->|cellmask| 10;\n 11[\"Single Cell Phenotyping\"];\n 10 -->|outfile| 11;\n 2 -->|output| 11;\n 12[\"Vitessce Visualization\"];\n 11 -->|output| 12;\n 9 -->|renamed_image| 12;\n 6 -->|mask| 12;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN_Exemplar_002_TMA_workflow",
"outputs": [
{
@@ -368178,7 +334200,6 @@
"id": "imaging/tutorial-CP",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -368200,7 +334221,7 @@
"How to segment cell nucleoli using CellProfiler in Galaxy.",
"How to extract features for images, nuclei and nucleoli."
],
- "pageviews": 6184230,
+ "pageviews": 6207196,
"pub_date": "2020-07-01",
"questions": [
"How do I run an image analysis pipeline on public data using CellProfiler?",
@@ -368216,26 +334237,26 @@
],
"short_id": "T00183",
"short_tools": [
- "idr_download_by_ids",
- "cp_display_data_on_image",
+ "cp_measure_image_area_occupied",
"cp_mask_image",
+ "cp_save_images",
"cp_measure_object_size_shape",
- "cp_measure_image_quality",
- "cp_enhance_or_suppress_features",
- "cp_measure_image_intensity",
+ "cp_measure_texture",
"cp_relate_objects",
- "cp_save_images",
"cp_image_math",
+ "cp_export_to_spreadsheet",
+ "cp_measure_granularity",
+ "cp_measure_image_quality",
"cp_convert_objects_to_image",
- "cp_measure_texture",
+ "cp_measure_image_intensity",
"cp_measure_object_intensity",
- "cp_measure_granularity",
- "cp_measure_image_area_occupied",
"cp_gray_to_color",
- "cp_common",
"cp_identify_primary_objects",
- "cp_export_to_spreadsheet",
- "cp_cellprofiler"
+ "cp_common",
+ "cp_display_data_on_image",
+ "cp_cellprofiler",
+ "idr_download_by_ids",
+ "cp_enhance_or_suppress_features"
],
"slides": true,
"slides_recordings": false,
@@ -368258,11 +334279,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -368297,6 +334313,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -368352,10 +334372,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -368402,11 +334418,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -368451,6 +334462,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -368503,10 +334518,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -368552,13 +334563,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
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- ]
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -368603,6 +334607,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -368655,10 +334663,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -368704,13 +334708,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -368755,6 +334752,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -368807,10 +334808,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -368856,13 +334853,6 @@
"state": "exact",
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -368907,6 +334897,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -368959,10 +334953,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369008,13 +334998,6 @@
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},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369059,6 +335042,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369111,10 +335098,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369160,13 +335143,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369211,6 +335187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369263,10 +335243,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369312,13 +335288,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369363,6 +335332,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369415,10 +335388,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369464,13 +335433,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369515,6 +335477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369567,10 +335533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369616,13 +335578,6 @@
"state": "exact",
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369667,6 +335622,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369719,10 +335678,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369768,13 +335723,6 @@
"state": "exact",
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- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369819,6 +335767,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -369871,10 +335823,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -369920,13 +335868,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -369971,6 +335912,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370023,10 +335968,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370072,13 +336013,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370123,6 +336057,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370175,10 +336113,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370224,13 +336158,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370275,6 +336202,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370327,10 +336258,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370376,13 +336303,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370427,6 +336347,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370479,10 +336403,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370528,13 +336448,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370579,6 +336492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370631,10 +336548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370680,13 +336593,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370731,6 +336637,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370783,10 +336693,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370832,13 +336738,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -370883,6 +336782,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -370935,10 +336838,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -370984,13 +336883,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -371035,6 +336927,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -371087,10 +336983,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -371136,13 +337028,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -371187,6 +337072,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -371239,10 +337128,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -371288,13 +337173,6 @@
"state": "exact",
"version": "3.1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.9+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -371339,6 +337217,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -371391,10 +337273,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -371440,14 +337318,6 @@
"state": "exact",
"version": "0.41"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.45",
- "0.44.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -371522,8 +337392,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 230,
- "visitors": 2245937,
+ "visit_duration": 229,
+ "visitors": 2256765,
"workflows": [
{
"creators": [],
@@ -371589,7 +337459,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"Starting modules\"];\n 1[\"Download images\"];\n 2[\"Segment complete nuclei\"];\n 0 -->|output_pipeline| 2;\n 3[\"Segmentation mask complete nuclei\"];\n 2 -->|output_pipeline| 3;\n 4[\"Label nuclei\"];\n 3 -->|output_pipeline| 4;\n 5[\"Save labelled nuclei\"];\n 4 -->|output_pipeline| 5;\n 6[\"Detect dark holes in nuclei\"];\n 5 -->|output_pipeline| 6;\n 7[\"Segment nucleoli that fall inside nuclei\"];\n 6 -->|output_pipeline| 7;\n 8[\"Segment nucleoli\"];\n 7 -->|output_pipeline| 8;\n 9[\"Convert the segmented nucleoli into an image\"];\n 8 -->|output_pipeline| 9;\n 10[\"Combine masks nuclei + nucleoli\"];\n 9 -->|output_pipeline| 10;\n 11[\"Save combined segmentation masks\"];\n 10 -->|output_pipeline| 11;\n 12[\"Segment all nuclei\"];\n 11 -->|output_pipeline| 12;\n 13[\"Segmentation mask nucleoli including cells touching borders\"];\n 12 -->|output_pipeline| 13;\n 14[\"Extract background\"];\n 13 -->|output_pipeline| 14;\n 15[\"Measure the image granularity\"];\n 14 -->|output_pipeline| 15;\n 16[\"Measure the nuclei texture\"];\n 15 -->|output_pipeline| 16;\n 17[\"Measure the nuclei intensity\"];\n 16 -->|output_pipeline| 17;\n 18[\"Measure size and shape of nuclei and nucleoli\"];\n 17 -->|output_pipeline| 18;\n 19[\"Relate nucleoli with their parent nuclei\"];\n 18 -->|output_pipeline| 19;\n 20[\"Measure the image quality\"];\n 19 -->|output_pipeline| 20;\n 21[\"Measure the area occupied by nuclei and nucleoli\"];\n 20 -->|output_pipeline| 21;\n 22[\"Measure the image intensity\"];\n 21 -->|output_pipeline| 22;\n 23[\"Export measurements\"];\n 22 -->|output_pipeline| 23;\n 24[\"Run CellProfiler\"];\n 1 -->|output_tar| 24;\n 23 -->|output_pipeline| 24;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "CP_pipeline_IDR_training",
"outputs": [
{
@@ -373083,10 +338953,10 @@
],
"dir": "topics/imaging/tutorials/hela-screen-analysis",
"edam_operation": [
- "Image analysis",
- "Visualisation",
+ "Image annotation",
"Data handling",
- "Image annotation"
+ "Image analysis",
+ "Visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -373131,7 +339001,7 @@
"How to extract features from an imaging screen in Galaxy.",
"How to analyse extracted features from an imaging screen in Galaxy."
],
- "pageviews": 774,
+ "pageviews": 776,
"pub_date": "2019-08-13",
"questions": [
"How do I analyze a HeLa fluorescence siRNA screen?",
@@ -373152,13 +339022,13 @@
],
"short_id": "T00180",
"short_tools": [
- "ip_2d_feature_extraction",
- "unzip",
"ip_2d_filter_segmentation_by_features",
"ip_filter_standard",
- "ip_binary_to_labelimage",
"ip_threshold",
- "collapse_dataset"
+ "collapse_dataset",
+ "unzip",
+ "ip_binary_to_labelimage",
+ "ip_2d_feature_extraction"
],
"slides": false,
"slides_recordings": false,
@@ -373215,6 +339085,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -373270,10 +339144,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -373320,11 +339190,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -373369,6 +339234,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -373421,10 +339290,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -373457,8 +339322,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.0.4",
- "0.0.3"
+ "0.0.3",
+ "0.0.4"
]
},
{
@@ -373474,11 +339339,6 @@
"state": "exact",
"version": "0.18.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.18.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -373526,6 +339386,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -373578,10 +339442,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -373629,10 +339489,6 @@
"state": "exact",
"version": "0.18.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -373679,6 +339535,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -373731,10 +339591,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -373782,10 +339638,6 @@
"state": "exact",
"version": "0.0.1-4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -373832,6 +339684,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -373884,10 +339740,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -373936,11 +339788,6 @@
"state": "exact",
"version": "1.12.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.12.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -373988,6 +339835,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -374040,10 +339891,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -374091,10 +339938,6 @@
"state": "exact",
"version": "0.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -374142,6 +339985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -374197,10 +340044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -374246,11 +340089,6 @@
"state": "exact",
"version": "6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -374297,6 +340135,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -374351,10 +340193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -374402,11 +340240,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -374466,7 +340299,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 153,
- "visitors": 599,
+ "visitors": 601,
"workflows": [
{
"creators": [
@@ -374607,7 +340440,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ninput images\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"];\n style 2 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Collapse Collection\"];\n 2 -->|output| 3;\n 189572e7-e0e6-4818-91b1-441beced67a4[\"Output\\noutput\"];\n 3 --> 189572e7-e0e6-4818-91b1-441beced67a4;\n style 189572e7-e0e6-4818-91b1-441beced67a4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "analyze_screen",
"outputs": [
{
@@ -374827,7 +340660,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ninput image\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nfilter rules\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Filter 2-D image\"];\n 0 -->|output| 2;\n 3[\"Threshold image\"];\n 2 -->|output| 3;\n 4[\"Convert binary image to label map\"];\n 3 -->|output| 4;\n 5[\"Extract image features\"];\n 4 -->|output| 5;\n 6[\"Filter label map by rules\"];\n 5 -->|output| 6;\n 4 -->|output| 6;\n 1 -->|output| 6;\n f6f7f638-0f3c-404e-ab2e-5281a0393060[\"Output\\noutput\"];\n 6 --> f6f7f638-0f3c-404e-ab2e-5281a0393060;\n style f6f7f638-0f3c-404e-ab2e-5281a0393060 stroke:#2c3143,stroke-width:4px;\n 7[\"Extract image features\"];\n 6 -->|output| 7;\n 0 -->|output| 7;\n 31da5e27-19fe-465e-95f0-96d3f6dcaba4[\"Output\\noutput\"];\n 7 --> 31da5e27-19fe-465e-95f0-96d3f6dcaba4;\n style 31da5e27-19fe-465e-95f0-96d3f6dcaba4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "feature_extraction",
"outputs": [
{
@@ -375177,7 +341010,7 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Locate bioimage data repositories",
"Compare repositories to find which are suitable for your data",
@@ -375185,7 +341018,7 @@
],
"pageviews": 0,
"priority": 4,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
"What are the commonly used repositories for bioimaging data?",
"Which repositories are suitable for my data?",
@@ -375476,16 +341309,16 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Organise bioimage metadata",
"Find out what REMBI is and why it is useful",
"Categorise what metadata belongs to each of the submodules of REMBI",
"Gather the metadata for an example bioimage dataset"
],
- "pageviews": 0,
+ "pageviews": 1,
"priority": 5,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
"What is REMBI and why should I use it?",
"What information should be included when collecting bioimage data?"
@@ -375582,7 +341415,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 0,
- "visitors": 0,
+ "visitors": 1,
"zenodo_link": ""
},
{
@@ -376253,7 +342086,6 @@
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -376288,7 +342120,7 @@
"Learn how to create a workflow",
"Learn how to share your work"
],
- "pageviews": 30721,
+ "pageviews": 30742,
"pub_date": "2016-03-29",
"questions": [
"How to use Galaxy?",
@@ -376296,16 +342128,16 @@
],
"short_id": "T00189",
"short_tools": [
- "CONVERTER_interval_to_bed_0",
+ "tp_sort_header_tool",
+ "Cut1",
"tp_replace_in_column",
- "get_flanks1",
+ "gops_intersect_1",
+ "tp_tail_tool",
+ "CONVERTER_interval_to_bed_0",
"Add_a_column1",
- "tp_sort_header_tool",
- "upload1",
"Grouping1",
- "tp_tail_tool",
- "gops_intersect_1",
- "Cut1"
+ "get_flanks1",
+ "upload1"
],
"slides": false,
"slides_recordings": false,
@@ -376317,11 +342149,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -376368,6 +342195,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -376423,10 +342254,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -376473,11 +342300,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -376522,6 +342344,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -376574,10 +342400,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -376618,10 +342440,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -376664,6 +342482,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -376716,10 +342538,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -376760,10 +342578,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -376806,6 +342620,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -376858,10 +342676,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -376902,10 +342716,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -376948,6 +342758,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377002,10 +342816,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -377052,11 +342862,6 @@
"state": "exact",
"version": "1.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -377102,6 +342907,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377156,10 +342965,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -377206,11 +343011,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -377256,6 +343056,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377310,10 +343114,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -377360,11 +343160,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -377410,6 +343205,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377468,10 +343267,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -377521,11 +343316,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -377573,6 +343363,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377633,10 +343427,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -377670,9 +343460,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -377686,11 +343476,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -377736,6 +343521,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377788,10 +343577,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -377835,11 +343620,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -377885,6 +343665,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -377937,10 +343721,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -377985,11 +343765,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -378035,6 +343810,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -378087,10 +343866,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -378131,10 +343906,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -378192,7 +343963,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 199,
- "visitors": 18401,
+ "visitors": 18418,
"workflows": [
{
"creators": [],
@@ -378203,7 +343974,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n 2[label=\"Select last\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Replace Text\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"Get flanks\"]\n 1 -> 4 [label=\"output\"]\n 5[label=\"Replace Text\"]\n 3 -> 5 [label=\"outfile\"]\n 6[label=\"Replace Text\"]\n 5 -> 6 [label=\"outfile\"]\n 7[label=\"Convert Genomic Intervals To BED\"]\n 6 -> 7 [label=\"outfile\"]\n 8[label=\"Intersect\"]\n 4 -> 8 [label=\"out_file1\"]\n 7 -> 8 [label=\"output1\"]\n 9[label=\"Group\"]\n 8 -> 9 [label=\"output\"]\n k9c25384759a14c45b05a17df644a9329[color=lightseagreen,label=\"Output\\nchr_count\"]\n 9 -> k9c25384759a14c45b05a17df644a9329\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n 2[label=\"Select last\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Replace Text\"]\n 0 -> 3 [label=\"output\"]\n 4[label=\"Get flanks\"]\n 1 -> 4 [label=\"output\"]\n 5[label=\"Replace Text\"]\n 3 -> 5 [label=\"outfile\"]\n 6[label=\"Replace Text\"]\n 5 -> 6 [label=\"outfile\"]\n 7[label=\"Convert Genomic Intervals To BED\"]\n 6 -> 7 [label=\"outfile\"]\n 8[label=\"Intersect\"]\n 4 -> 8 [label=\"out_file1\"]\n 7 -> 8 [label=\"output1\"]\n 9[label=\"Group\"]\n 8 -> 9 [label=\"output\"]\n kf6633d0aee3142329b68f22fbf3adae4[color=lightseagreen,label=\"Output\\nchr_count\"]\n 9 -> kf6633d0aee3142329b68f22fbf3adae4\n}",
"history": [
{
"hash": "48c2e99e6ac6b3f944b81c5725182a61c3a85d81",
@@ -378268,8 +344039,8 @@
}
],
"license": null,
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Select last\"];\n 0 -->|output| 2;\n 3[\"Replace Text\"];\n 0 -->|output| 3;\n 4[\"Get flanks\"];\n 1 -->|output| 4;\n 5[\"Replace Text\"];\n 3 -->|outfile| 5;\n 6[\"Replace Text\"];\n 5 -->|outfile| 6;\n 7[\"Convert Genomic Intervals To BED\"];\n 6 -->|outfile| 7;\n 8[\"Intersect\"];\n 4 -->|out_file1| 8;\n 7 -->|output1| 8;\n 9[\"Group\"];\n 8 -->|output| 9;\n 9c253847-59a1-4c45-b05a-17df644a9329[\"Output\\nchr_count\"];\n 9 --> 9c253847-59a1-4c45-b05a-17df644a9329;\n style 9c253847-59a1-4c45-b05a-17df644a9329 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Select last\"];\n 0 -->|output| 2;\n 3[\"Replace Text\"];\n 0 -->|output| 3;\n 4[\"Get flanks\"];\n 1 -->|output| 4;\n 5[\"Replace Text\"];\n 3 -->|outfile| 5;\n 6[\"Replace Text\"];\n 5 -->|outfile| 6;\n 7[\"Convert Genomic Intervals To BED\"];\n 6 -->|outfile| 7;\n 8[\"Intersect\"];\n 4 -->|out_file1| 8;\n 7 -->|output1| 8;\n 9[\"Group\"];\n 8 -->|output| 9;\n f6633d0a-ee31-4232-9b68-f22fbf3adae4[\"Output\\nchr_count\"];\n 9 --> f6633d0a-ee31-4232-9b68-f22fbf3adae4;\n style f6633d0a-ee31-4232-9b68-f22fbf3adae4 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Galaxy Introduction Peaks2Genes - Part 1",
"outputs": [
{
@@ -378306,7 +344077,7 @@
{
"label": "chr_count",
"output_name": "out_file1",
- "uuid": "9c253847-59a1-4c45-b05a-17df644a9329"
+ "uuid": "f6633d0a-ee31-4232-9b68-f22fbf3adae4"
}
]
}
@@ -378806,7 +344577,6 @@
"UseGalaxy.be",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -378837,7 +344607,7 @@
"Learn some of the basic concepts of genomics and bioinformatics",
"Familiarize yourself with the basics of Galaxy"
],
- "pageviews": 28941,
+ "pageviews": 28971,
"pub_date": "2017-10-18",
"questions": [
"Do genes on opposite strands ever overlap? If so, how often?"
@@ -378870,11 +344640,11 @@
],
"short_id": "T00191",
"short_tools": [
- "tp_cat",
+ "cat1",
"Filter1",
+ "gops_intersect_1",
"gene2exon1",
- "cat1",
- "gops_intersect_1"
+ "tp_cat"
],
"slides": false,
"slides_recordings": false,
@@ -378896,11 +344666,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -378947,6 +344712,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -379002,10 +344771,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -379052,11 +344817,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -379101,6 +344861,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -379153,10 +344917,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -379197,10 +344957,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -379243,6 +344999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -379295,10 +345055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -379339,10 +345095,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -379385,6 +345137,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -379437,10 +345193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -379481,10 +345233,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -379527,6 +345275,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -379581,10 +345333,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -379631,11 +345379,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -379681,6 +345424,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -379733,10 +345480,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -379781,11 +345524,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -379840,7 +345578,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 212,
- "visitors": 17973,
+ "visitors": 18001,
"workflows": [
{
"creators": [],
@@ -379912,7 +345650,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Gene BED To Exon/Intron/Codon BED\"];\n 0 -->|output| 1;\n 2[\"Filter\"];\n 1 -->|out_file1| 2;\n 3[\"Filter\"];\n 1 -->|out_file1| 3;\n 4[\"Intersect\"];\n 2 -->|out_file1| 4;\n 3 -->|out_file1| 4;\n 5[\"Intersect\"];\n 3 -->|out_file1| 5;\n 2 -->|out_file1| 5;\n 6[\"Concatenate datasets\"];\n 5 -->|output| 6;\n 4 -->|output| 6;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Galaxy Intro Strands 2",
"outputs": [],
"parent_id": "introduction/galaxy-intro-strands",
@@ -380010,7 +345748,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Filter\"];\n 0 -->|output| 1;\n 2[\"Filter\"];\n 0 -->|output| 2;\n 3[\"Filter\"];\n 0 -->|output| 3;\n 4[\"Intersect\"];\n 2 -->|out_file1| 4;\n 3 -->|out_file1| 4;\n 5[\"Intersect\"];\n 3 -->|out_file1| 5;\n 2 -->|out_file1| 5;\n 6[\"Concatenate datasets\"];\n 5 -->|output| 6;\n 4 -->|output| 6;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Galaxy Intro Strands",
"outputs": [],
"parent_id": "introduction/galaxy-intro-strands",
@@ -380401,15 +346139,15 @@
],
"dir": "topics/introduction/tutorials/galaxy-intro-ngs-data-managment",
"edam_operation": [
- "Data handling",
+ "Validation",
"Sequencing quality control",
"Formatting",
- "Sequence alignment",
- "Validation",
+ "Data handling",
"SNP detection",
- "Read mapping",
- "Generation",
"Sequence contamination filtering",
+ "Generation",
+ "Read mapping",
+ "Sequence alignment",
"Genome indexing"
],
"edam_topic": [],
@@ -380426,7 +346164,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no"
],
"js_requirements": {
@@ -380450,7 +346187,7 @@
"Understand most common types of NGS-related datatypes",
"Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2"
],
- "pageviews": 30230,
+ "pageviews": 30422,
"pub_date": "2017-02-22",
"questions": [
"How to manipulate and process NGS data"
@@ -380471,21 +346208,21 @@
],
"short_id": "T00188",
"short_tools": [
- "Grep1",
- "picard_MarkDuplicates",
- "snpeff_sars_cov_2",
- "tp_cut_tool",
- "lofreq_viterbi",
+ "collapse_dataset",
+ "fastp",
"lofreq_indelqual",
+ "lofreq_viterbi",
"lofreq_call",
+ "bwa_mem",
"multiqc",
- "snpSift_extractFields",
+ "samtools_view",
+ "Grep1",
+ "picard_MarkDuplicates",
+ "tp_cut_tool",
+ "snpeff_sars_cov_2",
"fasterq_dump",
- "fastp",
"samtools_stats",
- "bwa_mem",
- "samtools_view",
- "collapse_dataset"
+ "snpSift_extractFields"
],
"slides": false,
"slides_recordings": false,
@@ -380524,11 +346261,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -380558,6 +346290,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -380613,10 +346349,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -380663,11 +346395,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -380712,6 +346439,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -380764,10 +346495,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -380808,10 +346535,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -380854,6 +346577,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -380908,10 +346635,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -380959,11 +346682,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381009,6 +346727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381066,10 +346788,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381117,11 +346835,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381170,6 +346883,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381227,10 +346944,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381280,11 +346993,6 @@
"state": "exact",
"version": "2.18.2.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381330,6 +347038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381390,10 +347102,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381442,11 +347150,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381492,6 +347195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381549,10 +347256,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381601,11 +347304,6 @@
"state": "exact",
"version": "0.20.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381654,6 +347352,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381707,10 +347409,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381748,8 +347446,8 @@
"versions": [
"2.1.3.1+galaxy2",
"2.1.3.1+galaxy1",
- "2.1.5+galaxy0",
- "2.1.3.1+galaxy0"
+ "2.1.3.1+galaxy0",
+ "2.1.5+galaxy0"
]
},
{
@@ -381764,11 +347462,6 @@
"state": "exact",
"version": "2.1.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381814,6 +347507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -381866,10 +347563,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -381918,11 +347611,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -381968,6 +347656,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382020,10 +347712,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -382068,11 +347756,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -382118,6 +347801,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382143,9 +347830,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -382182,10 +347869,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -382238,11 +347921,6 @@
"state": "exact",
"version": "1.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -382288,6 +347966,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382312,8 +347994,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -382347,10 +348029,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -382402,11 +348080,6 @@
"state": "exact",
"version": "1.9+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -382452,6 +348125,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382505,10 +348182,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -382553,11 +348226,6 @@
"state": "exact",
"version": "4.5covid19"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.5covid19"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -382603,6 +348271,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382657,10 +348329,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -382705,11 +348373,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -382755,6 +348418,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382810,10 +348477,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -382849,10 +348512,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.10.4",
- "2.10.4+galaxy1",
"2.10.7+galaxy1",
- "2.11.0+galaxy0"
+ "2.11.0+galaxy0",
+ "2.10.4",
+ "2.10.4+galaxy1"
]
},
{
@@ -382865,11 +348528,6 @@
"state": "exact",
"version": "2.10.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -382917,6 +348575,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -382970,10 +348632,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -383009,10 +348667,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.10.4",
- "2.10.4+galaxy1",
"2.10.7+galaxy1",
- "2.11.0+galaxy0"
+ "2.11.0+galaxy0",
+ "2.10.4",
+ "2.10.4+galaxy1"
]
},
{
@@ -383025,28 +348683,6 @@
"state": "exact",
"version": "2.10.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.1+galaxy0",
- "2.10.4",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.8+galaxy0",
- "3.0.5+galaxy0",
- "2.10.7+galaxy2",
- "3.0.3+galaxy0",
- "2.11.0+galaxy1",
- "3.1.1+galaxy1",
- "3.0.8+galaxy0",
- "3.1.0+galaxy1",
- "3.0.10+galaxy0",
- "3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -383094,6 +348730,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -383119,8 +348759,8 @@
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -383154,10 +348794,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -383207,21 +348843,13 @@
"state": "exact",
"version": "4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"4.2",
- "4.1",
- "5.1.0"
+ "5.1.0",
+ "4.1"
]
},
{
@@ -383264,6 +348892,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -383318,10 +348950,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -383369,11 +348997,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -383439,8 +349062,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 200,
- "visitors": 17202,
+ "visit_duration": 201,
+ "visitors": 17325,
"workflows": [
{
"creators": [],
@@ -383536,7 +349159,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAccessions\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Faster Download and Extract Reads in FASTQ\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|list_paired| 3;\n 4[\"Map with BWA-MEM\"];\n 3 -->|output_paired_coll| 4;\n 1 -->|output| 4;\n 5[\"Samtools view\"];\n 4 -->|bam_output| 5;\n 6[\"MarkDuplicates\"];\n 5 -->|outputsam| 6;\n 7[\"Samtools stats\"];\n 6 -->|outFile| 7;\n 8[\"Realign reads\"];\n 6 -->|outFile| 8;\n 1 -->|output| 8;\n 9[\"MultiQC\"];\n 3 -->|report_json| 9;\n 6 -->|metrics_file| 9;\n 7 -->|output| 9;\n 10[\"Insert indel qualities\"];\n 8 -->|realigned| 10;\n 1 -->|output| 10;\n 11[\"Call variants\"];\n 10 -->|output| 11;\n 1 -->|output| 11;\n 12[\"SnpEff eff:\"];\n 11 -->|variants| 12;\n 13[\"SnpSift Extract Fields\"];\n 12 -->|snpeff_output| 13;\n 14[\"Collapse Collection\"];\n 13 -->|output| 14;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "NGS_tutorial",
"outputs": [
{
@@ -384613,7 +350236,6 @@
"inexact_supported_servers": [
"MISSISSIPPI",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no"
],
"js_requirements": {
@@ -384635,21 +350257,21 @@
"Learn how to run a published Galaxy workflow",
"Learn how histories can be inspected and re-used."
],
- "pageviews": 2497,
+ "pageviews": 2504,
"pub_date": "2021-08-25",
"questions": [
"How to reproduce published Galaxy results (workflows and histories)"
],
"short_id": "T00192",
"short_tools": [
- "datamash_ops",
+ "Cut1",
+ "csv_to_tabular",
+ "Grouping1",
"Remove beginning1",
+ "datamash_ops",
"ggplot2_point",
- "tp_sorted_uniq",
"upload1",
- "csv_to_tabular",
- "Grouping1",
- "Cut1"
+ "tp_sorted_uniq"
],
"slides": false,
"slides_recordings": false,
@@ -384688,11 +350310,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -384722,6 +350339,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -384777,10 +350398,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -384827,11 +350444,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -384876,6 +350488,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -384928,10 +350544,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -384972,10 +350584,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -385018,6 +350626,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -385070,10 +350682,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -385114,10 +350722,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -385160,6 +350764,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -385212,10 +350820,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -385256,10 +350860,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -385302,6 +350902,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -385354,10 +350958,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -385398,10 +350998,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -385444,6 +351040,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -385498,10 +351098,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -385548,11 +351144,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -385598,6 +351189,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -385655,10 +351250,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -385705,11 +351296,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -385755,6 +351341,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -385811,10 +351401,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -385863,18 +351449,6 @@
"state": "exact",
"version": "2.2.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1+galaxy2",
- "3.4.0+galaxy1",
- "3.3.5+galaxy2",
- "3.3.5+galaxy1",
- "3.3.5+galaxy0",
- "3.4.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -385894,10 +351468,10 @@
"versions": [
"2.2.1+galaxy2",
"3.4.0+galaxy1",
- "3.3.5+galaxy2",
+ "3.4.0+galaxy0",
"3.3.5+galaxy1",
"3.3.5+galaxy0",
- "3.4.0+galaxy0"
+ "3.3.5+galaxy2"
]
},
{
@@ -385930,6 +351504,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -385982,10 +351560,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -386026,10 +351600,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -386083,8 +351653,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 256,
- "visitors": 1835,
+ "visit_duration": 255,
+ "visitors": 1841,
"workflows": [
{
"creators": [],
@@ -386095,7 +351665,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n 1[label=\"Convert CSV to tabular\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"Datamash\"]\n 1 -> 2 [label=\"tabular\"]\n k4757af2c8d83441db6bda4bd9dcfdd74[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n 2 -> k4757af2c8d83441db6bda4bd9dcfdd74\n 3[label=\"Remove beginning\"]\n 1 -> 3 [label=\"tabular\"]\n 4[label=\"Cut\"]\n 3 -> 4 [label=\"out_file1\"]\n 5[label=\"Group\"]\n 3 -> 5 [label=\"out_file1\"]\n k7cc06f2c87b349649b508908fec7cf6f[color=lightseagreen,label=\"Output\\ngroup1\"]\n 5 -> k7cc06f2c87b349649b508908fec7cf6f\n 6[label=\"Group\"]\n 3 -> 6 [label=\"out_file1\"]\n ke9760e604fdb4b44b373743c1bd828a1[color=lightseagreen,label=\"Output\\ngroup2\"]\n 6 -> ke9760e604fdb4b44b373743c1bd828a1\n 7[label=\"Scatterplot w ggplot2\"]\n 3 -> 7 [label=\"out_file1\"]\n 8[label=\"Scatterplot w ggplot2\"]\n 3 -> 8 [label=\"out_file1\"]\n 9[label=\"Unique\"]\n 4 -> 9 [label=\"out_file1\"]\n kec39c0adeb2647d6b9a7c2e5ffa043c6[color=lightseagreen,label=\"Output\\nunique_output\"]\n 9 -> kec39c0adeb2647d6b9a7c2e5ffa043c6\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n 1[label=\"Convert CSV to tabular\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"Datamash\"]\n 1 -> 2 [label=\"tabular\"]\n kd74b3ccf3cfe4b3da56070c654798134[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n 2 -> kd74b3ccf3cfe4b3da56070c654798134\n 3[label=\"Remove beginning\"]\n 1 -> 3 [label=\"tabular\"]\n 4[label=\"Cut\"]\n 3 -> 4 [label=\"out_file1\"]\n 5[label=\"Group\"]\n 3 -> 5 [label=\"out_file1\"]\n k0af9987109eb4b6198e9b4e308383cbf[color=lightseagreen,label=\"Output\\ngroup1\"]\n 5 -> k0af9987109eb4b6198e9b4e308383cbf\n 6[label=\"Group\"]\n 3 -> 6 [label=\"out_file1\"]\n ke4a63107f1a6409dbb2b4ab82696f72c[color=lightseagreen,label=\"Output\\ngroup2\"]\n 6 -> ke4a63107f1a6409dbb2b4ab82696f72c\n 7[label=\"Scatterplot w ggplot2\"]\n 3 -> 7 [label=\"out_file1\"]\n 8[label=\"Scatterplot w ggplot2\"]\n 3 -> 8 [label=\"out_file1\"]\n 9[label=\"Unique\"]\n 4 -> 9 [label=\"out_file1\"]\n kec39c0adeb2647d6b9a7c2e5ffa043c6[color=lightseagreen,label=\"Output\\nunique_output\"]\n 9 -> kec39c0adeb2647d6b9a7c2e5ffa043c6\n}",
"history": [
{
"hash": "03bdb9f97f1f07b25cb24c182fce72381d420781",
@@ -386134,8 +351704,8 @@
}
],
"license": null,
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\niris\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Convert CSV to tabular\"];\n 0 -->|output| 1;\n 2[\"Datamash\"];\n 1 -->|tabular| 2;\n 4757af2c-8d83-441d-b6bd-a4bd9dcfdd74[\"Output\\ndatamash_output\"];\n 2 --> 4757af2c-8d83-441d-b6bd-a4bd9dcfdd74;\n style 4757af2c-8d83-441d-b6bd-a4bd9dcfdd74 stroke:#2c3143,stroke-width:4px;\n 3[\"Remove beginning\"];\n 1 -->|tabular| 3;\n 4[\"Cut\"];\n 3 -->|out_file1| 4;\n 5[\"Group\"];\n 3 -->|out_file1| 5;\n 7cc06f2c-87b3-4964-9b50-8908fec7cf6f[\"Output\\ngroup1\"];\n 5 --> 7cc06f2c-87b3-4964-9b50-8908fec7cf6f;\n style 7cc06f2c-87b3-4964-9b50-8908fec7cf6f stroke:#2c3143,stroke-width:4px;\n 6[\"Group\"];\n 3 -->|out_file1| 6;\n e9760e60-4fdb-4b44-b373-743c1bd828a1[\"Output\\ngroup2\"];\n 6 --> e9760e60-4fdb-4b44-b373-743c1bd828a1;\n style e9760e60-4fdb-4b44-b373-743c1bd828a1 stroke:#2c3143,stroke-width:4px;\n 7[\"Scatterplot w ggplot2\"];\n 3 -->|out_file1| 7;\n 8[\"Scatterplot w ggplot2\"];\n 3 -->|out_file1| 8;\n 9[\"Unique\"];\n 4 -->|out_file1| 9;\n ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n 9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\niris\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Convert CSV to tabular\"];\n 0 -->|output| 1;\n 2[\"Datamash\"];\n 1 -->|tabular| 2;\n d74b3ccf-3cfe-4b3d-a560-70c654798134[\"Output\\ndatamash_output\"];\n 2 --> d74b3ccf-3cfe-4b3d-a560-70c654798134;\n style d74b3ccf-3cfe-4b3d-a560-70c654798134 stroke:#2c3143,stroke-width:4px;\n 3[\"Remove beginning\"];\n 1 -->|tabular| 3;\n 4[\"Cut\"];\n 3 -->|out_file1| 4;\n 5[\"Group\"];\n 3 -->|out_file1| 5;\n 0af99871-09eb-4b61-98e9-b4e308383cbf[\"Output\\ngroup1\"];\n 5 --> 0af99871-09eb-4b61-98e9-b4e308383cbf;\n style 0af99871-09eb-4b61-98e9-b4e308383cbf stroke:#2c3143,stroke-width:4px;\n 6[\"Group\"];\n 3 -->|out_file1| 6;\n e4a63107-f1a6-409d-bb2b-4ab82696f72c[\"Output\\ngroup2\"];\n 6 --> e4a63107-f1a6-409d-bb2b-4ab82696f72c;\n style e4a63107-f1a6-409d-bb2b-4ab82696f72c stroke:#2c3143,stroke-width:4px;\n 7[\"Scatterplot w ggplot2\"];\n 3 -->|out_file1| 7;\n 8[\"Scatterplot w ggplot2\"];\n 3 -->|out_file1| 8;\n 9[\"Unique\"];\n 4 -->|out_file1| 9;\n ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n 9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Training: Galaxy 101 For Everyone",
"outputs": [
{
@@ -386184,7 +351754,7 @@
{
"label": "datamash_output",
"output_name": "out_file",
- "uuid": "4757af2c-8d83-441d-b6bd-a4bd9dcfdd74"
+ "uuid": "d74b3ccf-3cfe-4b3d-a560-70c654798134"
}
]
},
@@ -386228,7 +351798,7 @@
{
"label": "group1",
"output_name": "out_file1",
- "uuid": "7cc06f2c-87b3-4964-9b50-8908fec7cf6f"
+ "uuid": "0af99871-09eb-4b61-98e9-b4e308383cbf"
}
]
},
@@ -386272,7 +351842,7 @@
{
"label": "group2",
"output_name": "out_file1",
- "uuid": "e9760e60-4fdb-4b44-b373-743c1bd828a1"
+ "uuid": "e4a63107-f1a6-409d-bb2b-4ab82696f72c"
}
]
},
@@ -386764,7 +352334,7 @@
"Become comfortable converting text-based files in a variety of ways.",
"Reason about the expected outcome of tools"
],
- "pageviews": 6028,
+ "pageviews": 6054,
"pub_date": "2022-07-20",
"questions": [
"How can I do basic data manipulation in Galaxy?",
@@ -386773,24 +352343,24 @@
"short_id": "T00184",
"short_tools": [
"",
- "datamash_ops",
- "tp_cat",
- "Add_a_column1",
+ "cat1",
"tp_sort_header_tool",
- "tp_sorted_uniq",
- "upload1",
- "Grouping1",
- "Remove beginning1",
"Filter1",
- "join1",
"Cut1",
- "tp_split_on_column",
- "cat1",
"Show beginning1",
- "regexColumn1",
+ "Add_a_column1",
+ "tp_cat",
"Count1",
+ "tp_split_on_column",
+ "regexColumn1",
+ "tp_sorted_uniq",
"tabular_to_csv",
- "wc_gnu"
+ "Remove beginning1",
+ "datamash_ops",
+ "wc_gnu",
+ "Grouping1",
+ "join1",
+ "upload1"
],
"slides": false,
"slides_recordings": false,
@@ -386821,6 +352391,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -386876,10 +352450,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -386926,11 +352496,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -386975,6 +352540,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387027,10 +352596,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387071,10 +352636,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387117,6 +352678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387169,10 +352734,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387213,10 +352774,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387259,6 +352816,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387311,10 +352872,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387355,10 +352912,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387401,6 +352954,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387453,10 +353010,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387497,10 +353050,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387543,6 +353092,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387595,10 +353148,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387639,10 +353188,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387685,6 +353230,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387737,10 +353286,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387781,10 +353326,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387827,6 +353368,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -387879,10 +353424,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -387923,10 +353464,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -387969,6 +353506,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -388021,10 +353562,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -388065,10 +353602,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -388111,6 +353644,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -388163,10 +353700,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -388207,10 +353740,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -388253,6 +353782,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -388308,10 +353841,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -388354,11 +353883,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -388406,6 +353930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -388460,10 +353988,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -388512,11 +354036,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -388562,6 +354081,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -388616,10 +354139,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -388666,11 +354185,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -388716,6 +354230,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -388770,10 +354288,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -388820,11 +354334,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -388870,6 +354379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -388927,10 +354440,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -388966,9 +354475,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -388976,8 +354485,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -388986,11 +354495,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -389036,6 +354540,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -389092,10 +354600,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -389144,11 +354648,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -389196,6 +354695,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -389253,10 +354756,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -389303,11 +354802,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -389353,6 +354847,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -389412,10 +354910,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -389470,11 +354964,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -389520,6 +355009,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -389572,10 +355065,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -389616,10 +355105,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -389662,6 +355147,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -389714,10 +355203,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -389758,10 +355243,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -389805,145 +355286,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
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- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "local"
- },
- {
- "id": "",
- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
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- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -389998,10 +355341,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -390042,10 +355381,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390088,6 +355423,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -390140,10 +355479,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -390184,10 +355519,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390230,6 +355561,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -390282,10 +355617,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -390326,10 +355657,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390372,6 +355699,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -390424,10 +355755,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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"state": "missing"
@@ -390468,10 +355795,6 @@
"server": "https://usegalaxy.eu",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390514,6 +355837,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
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"server": "https://usegalaxy.eu",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390656,6 +355975,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -390708,10 +356031,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -390752,10 +356071,6 @@
"server": "https://usegalaxy.eu",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390798,6 +356113,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -390850,10 +356169,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -390894,10 +356209,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -390940,6 +356251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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@@ -392521,7 +357930,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
"outputs": [],
"parent_id": "introduction/data-manipulation-olympics",
@@ -392574,26 +357983,6 @@
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@@ -393977,7 +358632,7 @@
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],
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"video_view": 0,
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},
{
"admin_install": {
@@ -394570,9 +359225,9 @@
],
"dir": "topics/introduction/tutorials/galaxy-intro-short",
"edam_operation": [
+ "Sequencing quality control",
"Sequence composition calculation",
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],
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"exact_supported_servers": [
@@ -394589,7 +359244,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
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"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -394619,7 +359273,7 @@
"Learn how to extract and run a workflow",
"Learn how to share a history"
],
- "pageviews": 6244338,
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"questions": [
@@ -394627,8 +359281,8 @@
],
"short_id": "T00190",
"short_tools": [
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- "cshl_fastq_quality_filter"
+ "cshl_fastq_quality_filter",
+ "fastqc"
],
"slides": true,
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@@ -394672,11 +359326,6 @@
"url": "https://usegalaxy.cz/",
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},
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- "url": "https://usegalaxy.fr/",
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -394711,6 +359360,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -394766,10 +359419,6 @@
"name": "InteractoMIX",
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},
- {
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -394816,11 +359465,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -394865,6 +359509,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -394924,10 +359572,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -394977,15 +359621,6 @@
"state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -395038,6 +359673,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -395095,10 +359734,6 @@
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -395134,8 +359769,8 @@
"versions": [
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"1.0.0",
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- "1.0.1"
+ "1.0.1",
+ "1.0.2"
]
},
{
@@ -395148,11 +359783,6 @@
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"version": "1.0.2+galaxy2"
},
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- "state": "exact",
- "version": "1.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -395200,6 +359830,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -395261,10 +359895,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -395315,9 +359945,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
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"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -395328,11 +359958,6 @@
"state": "exact",
"version": "0.72"
},
- {
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- "state": "exact",
- "version": "0.72"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -395381,6 +360006,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -395406,8 +360035,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -395446,10 +360075,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -395475,8 +360100,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -395505,9 +360130,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -395518,11 +360143,6 @@
"state": "exact",
"version": "0.74+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -395585,8 +360205,8 @@
"video": true,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 421,
- "visitors": 2284316,
+ "visit_duration": 422,
+ "visitors": 2295356,
"workflows": [
{
"creators": [],
@@ -395597,7 +360217,7 @@
"report": null,
"subworkflows": false
},
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{
"hash": "bcd92cb059319065ea797c48e5e68c47ceae2dbd",
@@ -395664,8 +360284,8 @@
}
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n 2[\"Filter by quality\"];\n 0 -->|output| 2;\n 9cbd4410-c869-434b-bdd4-f377b8862dc2[\"Output\\nfilter1\"];\n 2 --> 9cbd4410-c869-434b-bdd4-f377b8862dc2;\n style 9cbd4410-c869-434b-bdd4-f377b8862dc2 stroke:#2c3143,stroke-width:4px;\n 3[\"Filter by quality\"];\n 0 -->|output| 3;\n 30da732b-2c94-428d-845b-1e9aba13fdb0[\"Output\\nfilter2\"];\n 3 --> 30da732b-2c94-428d-845b-1e9aba13fdb0;\n style 30da732b-2c94-428d-845b-1e9aba13fdb0 stroke:#2c3143,stroke-width:4px;",
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"name": "Galaxy Intro Short",
"outputs": [
{
@@ -395708,7 +360328,7 @@
{
"label": "filter1",
"output_name": "output",
- "uuid": "d59c759a-b15f-4b37-baca-3a7868258b36"
+ "uuid": "9cbd4410-c869-434b-bdd4-f377b8862dc2"
}
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@@ -395752,7 +360372,7 @@
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"output_name": "output",
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]
}
@@ -396449,7 +361069,11 @@
"Mapping"
],
"edam_topic": [],
- "exact_supported_servers": [],
+ "exact_supported_servers": [
+ "UseGalaxy.cz",
+ "UseGalaxy.eu",
+ "UseGalaxy.org (Main)"
+ ],
"feedback_mean_note": null,
"feedback_number": 0,
"hands_on": true,
@@ -396459,11 +361083,7 @@
"GalaxyTrakr",
"MISSISSIPPI",
"UseGalaxy.be",
- "UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr",
- "UseGalaxy.no",
- "UseGalaxy.org (Main)"
+ "UseGalaxy.no"
],
"js_requirements": {
"mathjax": null,
@@ -396479,7 +361099,7 @@
"layout": "tutorial_hands_on",
"level": "Introductory",
"license": "CC-BY-4.0",
- "mod_date": "2024-10-15",
+ "mod_date": "2024-12-11",
"objectives": [
"Familiarize yourself with the basics of Galaxy",
"Learn how to obtain data from external sources",
@@ -396488,7 +361108,7 @@
"Learn how to create a workflow",
"Learn how to share your work"
],
- "pageviews": 59803,
+ "pageviews": 60049,
"priority": 2,
"pub_date": "2016-12-19",
"questions": [
@@ -396522,18 +361142,34 @@
],
"short_id": "T00186",
"short_tools": [
- "datamash_ops",
"tp_sort_header_tool",
- "upload1",
- "comp1",
"bedtools_intersectbed",
- "tp_head_tool"
+ "tp_head_tool",
+ "datamash_ops",
+ "comp1",
+ "upload1"
],
"slides": false,
"slides_recordings": false,
"subtopic": "core",
"supported_servers": {
- "exact": [],
+ "exact": [
+ {
+ "name": "UseGalaxy.cz",
+ "url": "https://usegalaxy.cz/",
+ "usegalaxy": false
+ },
+ {
+ "name": "UseGalaxy.eu",
+ "url": "https://usegalaxy.eu",
+ "usegalaxy": true
+ },
+ {
+ "name": "UseGalaxy.org (Main)",
+ "url": "https://usegalaxy.org",
+ "usegalaxy": true
+ }
+ ],
"inexact": [
{
"name": "Galaxy@AuBi",
@@ -396555,30 +361191,10 @@
"url": "https://usegalaxy.be/",
"usegalaxy": false
},
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- "url": "https://usegalaxy.cz/",
- "usegalaxy": false
- },
- {
- "name": "UseGalaxy.eu",
- "url": "https://usegalaxy.eu",
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- },
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.org (Main)",
- "url": "https://usegalaxy.org",
- "usegalaxy": true
}
]
},
@@ -396604,6 +361220,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -396659,10 +361279,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -396709,11 +361325,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -396758,6 +361369,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
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"server": "http://galaxy.interactomix.com/",
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -396854,10 +361465,6 @@
"server": "https://usegalaxy.eu",
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},
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- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -396900,6 +361507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -396954,10 +361565,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
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"state": "exact",
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},
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -397054,6 +361656,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -397108,10 +361714,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
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},
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- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
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},
{
- "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1sort1",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
"servers": [
{
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@@ -397209,190 +361806,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
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- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
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- "server": "http://hyperbrowser.uio.no/hb/",
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- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
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- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
- "9.3+galaxy1"
- ]
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "1.0.0",
- "1.1.0"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "1.1.0"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "9.3+galaxy1",
- "1.0.0",
- "1.1.0",
- "9.3+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "9.3+galaxy1",
- "9.3+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "1.1.0"
- ]
- },
- {
- "server": "https://usegalaxy.org",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "9.3+galaxy1",
- "1.0.0",
- "1.1.0"
- ]
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "inexact",
- "versions": [
- "1.1.1",
- "9.3+galaxy1",
- "9.3+galaxy0"
- ]
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "1.1.1sort1"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -397455,10 +361869,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -397497,10 +361907,10 @@
"2.29.2",
"2.30.0",
"2.31.1+galaxy0",
- "2.27.1+galaxy1",
"2.19.0",
"2.29.0",
- "2.24.0"
+ "2.24.0",
+ "2.27.1+galaxy1"
]
},
{
@@ -397513,11 +361923,6 @@
"state": "exact",
"version": "2.30.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -397567,6 +361972,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -397624,10 +362033,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -397674,11 +362079,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -397724,6 +362124,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -397784,10 +362188,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -397835,11 +362235,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -397890,6 +362285,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -397942,10 +362341,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -397986,10 +362381,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -398018,7 +362409,6 @@
"comp1",
"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
"toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
- "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1sort1",
"toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
"toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
"toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
@@ -398039,12 +362429,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json"
},
- "version": 65,
+ "version": 66,
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 205,
- "visitors": 35834,
+ "visit_duration": 204,
+ "visitors": 36002,
"workflows": [
{
"creators": [
@@ -398183,7 +362573,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nFeatures\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"bedtools Intersect intervals\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Datamash\"];\n 2 -->|output| 3;\n 4[\"Sort\"];\n 3 -->|out_file| 4;\n 5[\"Select first\"];\n 4 -->|outfile| 5;\n 6[\"Compare two Datasets\"];\n 0 -->|output| 6;\n 5 -->|outfile| 6;\n 565e3d76-0230-4a5e-87c1-9c36ce0b7df8[\"Output\\ntop_5_exons\"];\n 6 --> 565e3d76-0230-4a5e-87c1-9c36ce0b7df8;\n style 565e3d76-0230-4a5e-87c1-9c36ce0b7df8 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Find exons with the highest number of features",
"outputs": [
{
@@ -399797,7 +364187,6 @@
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -399835,7 +364224,7 @@
"Learn how to create a workflow",
"Learn how to share your work"
],
- "pageviews": 26829,
+ "pageviews": 26922,
"priority": 2,
"pub_date": "2019-11-14",
"questions": [
@@ -399870,14 +364259,14 @@
],
"short_id": "T00187",
"short_tools": [
- "datamash_ops",
+ "Cut1",
+ "csv_to_tabular",
+ "Grouping1",
"Remove beginning1",
+ "datamash_ops",
"ggplot2_point",
- "tp_sorted_uniq",
"upload1",
- "csv_to_tabular",
- "Grouping1",
- "Cut1"
+ "tp_sorted_uniq"
],
"slides": false,
"slides_recordings": false,
@@ -399889,11 +364278,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -399950,6 +364334,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -400005,10 +364393,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -400055,11 +364439,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -400104,6 +364483,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -400156,10 +364539,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -400200,10 +364579,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -400246,6 +364621,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -400298,10 +364677,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -400342,10 +364717,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -400388,6 +364759,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -400440,10 +364815,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -400484,10 +364855,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -400530,6 +364897,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -400582,10 +364953,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -400626,10 +364993,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -400672,6 +365035,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -400726,10 +365093,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -400776,11 +365139,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -400826,6 +365184,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -400883,10 +365245,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -400933,11 +365291,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -400983,6 +365336,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -401041,10 +365398,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -401082,8 +365435,8 @@
"versions": [
"2.2.1+galaxy1",
"2.2.1+galaxy2",
- "2.2.1+galaxy0",
- "2.2.1"
+ "2.2.1",
+ "2.2.1+galaxy0"
]
},
{
@@ -401098,11 +365451,6 @@
"state": "exact",
"version": "3.3.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -401148,6 +365496,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -401200,10 +365552,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -401244,10 +365592,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -401302,7 +365646,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 250,
- "visitors": 16284,
+ "visitors": 16356,
"workflows": [
{
"creators": [],
@@ -401450,7 +365794,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\niris\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Convert CSV to tabular\"];\n 0 -->|output| 1;\n 2[\"Datamash\"];\n 1 -->|tabular| 2;\n 254f1b4b-d466-4f0e-8c46-0e97bbedae4d[\"Output\\ndatamash_output\"];\n 2 --> 254f1b4b-d466-4f0e-8c46-0e97bbedae4d;\n style 254f1b4b-d466-4f0e-8c46-0e97bbedae4d stroke:#2c3143,stroke-width:4px;\n 3[\"Remove beginning\"];\n 1 -->|tabular| 3;\n 4[\"Cut\"];\n 3 -->|out_file1| 4;\n 5[\"Group\"];\n 3 -->|out_file1| 5;\n a689bddf-14d0-4a72-b1f9-c34d8f50d2b3[\"Output\\ngroup1\"];\n 5 --> a689bddf-14d0-4a72-b1f9-c34d8f50d2b3;\n style a689bddf-14d0-4a72-b1f9-c34d8f50d2b3 stroke:#2c3143,stroke-width:4px;\n 6[\"Group\"];\n 3 -->|out_file1| 6;\n ac7c73b2-58dd-4c6e-85ce-ddf49323b206[\"Output\\ngroup2\"];\n 6 --> ac7c73b2-58dd-4c6e-85ce-ddf49323b206;\n style ac7c73b2-58dd-4c6e-85ce-ddf49323b206 stroke:#2c3143,stroke-width:4px;\n 7[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 7;\n 8[\"Scatterplot with ggplot2\"];\n 3 -->|out_file1| 8;\n 9[\"Unique\"];\n 4 -->|out_file1| 9;\n 8a2b5e30-d42a-4019-9674-4b4af00c820a[\"Output\\nunique_output\"];\n 9 --> 8a2b5e30-d42a-4019-9674-4b4af00c820a;\n style 8a2b5e30-d42a-4019-9674-4b4af00c820a stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GTN Training: Galaxy 101 For Everyone",
"outputs": [
{
@@ -401817,18 +366161,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastp\n owner: iuc\n revisions: 65b93b623c77\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json",
- "contributions": {
- "authorship": [
- "nekrut"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "bebatut",
- "nekrut",
- "natefoo"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -401837,121 +366169,14 @@
"name": "Anton Nekrutenko",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "anton@nekrut.org",
- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
- {
- "email": "nate@bx.psu.edu",
- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
}
],
"dir": "topics/introduction/tutorials/vsi_qc",
"draft": true,
"edam_operation": [
+ "Sequencing quality control",
"Validation",
- "Sequence contamination filtering",
- "Sequencing quality control"
+ "Sequence contamination filtering"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -401959,7 +366184,6 @@
"GalaxyTrakr",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -401987,7 +366211,7 @@
"Learn about fastp",
"Learn about multiqc"
],
- "pageviews": 201,
+ "pageviews": 204,
"priority": 10,
"pub_date": "2024-03-26",
"questions": [
@@ -401995,8 +366219,8 @@
],
"short_id": "T00436",
"short_tools": [
- "fastp",
- "multiqc"
+ "multiqc",
+ "fastp"
],
"slides": false,
"slides_recordings": false,
@@ -402023,11 +366247,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -402079,6 +366298,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -402134,10 +366357,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -402184,11 +366403,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -402233,6 +366447,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -402288,10 +366506,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -402329,11 +366543,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -402346,11 +366560,6 @@
"state": "exact",
"version": "0.23.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -402397,6 +366606,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -402451,10 +366664,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -402503,11 +366712,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -402518,8 +366722,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -402570,8 +366774,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 212,
- "visitors": 154,
+ "visit_duration": 233,
+ "visitors": 157,
"zenodo_link": "https://zenodo.org/records/10870107"
},
{
@@ -402784,7 +366988,7 @@
"Use pymuon-suite in Galaxy to find stopping sites",
"Understand the limitations of these tools and techniques"
],
- "pageviews": 203,
+ "pageviews": 204,
"priority": 2,
"pub_date": "2024-01-22",
"questions": [
@@ -402850,6 +367054,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -402905,10 +367113,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -402955,11 +367159,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -403004,6 +367203,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -403056,10 +367259,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -403102,10 +367301,6 @@
"state": "exact",
"version": "0.3.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -403148,6 +367343,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -403200,10 +367399,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -403246,10 +367441,6 @@
"state": "exact",
"version": "0.3.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -403298,7 +367489,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 156,
- "visitors": 134,
+ "visitors": 135,
"workflows": [
{
"creators": [
@@ -403424,7 +367615,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nCopper.castep\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"PyMuonSuite AIRSS UEP Optimise\"];\n 2 -->|output| 3;\n 1 -->|output| 3;\n 0 -->|output| 3;\n f3be7cd2-3974-49f2-aa0e-96c79b4ab34c[\"Output\\nAll muons in host material\"];\n 3 --> f3be7cd2-3974-49f2-aa0e-96c79b4ab34c;\n style f3be7cd2-3974-49f2-aa0e-96c79b4ab34c stroke:#2c3143,stroke-width:4px;\n 4[\"PyMuonSuite AIRSS Cluster\"];\n 3 -->|uep_results| 4;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
"outputs": [
{
@@ -403582,18 +367773,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: join_files_on_column_fuzzy\n owner: bgruening\n revisions: 22ec3c1a20cd\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_classification\n owner: galaxyp\n revisions: b574b84afc4d\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_combine\n owner: galaxyp\n revisions: 48c07268f341\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n owner: galaxyp\n revisions: 25b83cbd596a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_preprocessing\n owner: galaxyp\n revisions: ed9ed1e6cca2\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n owner: galaxyp\n revisions: 3b7a35d50ebf\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_segmentations\n owner: galaxyp\n revisions: 82f6c2f4332d\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_peak_detection\n owner: galaxyp\n revisions: e9300ef37403\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_preprocessing\n owner: galaxyp\n revisions: 71411ac28268\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json",
- "contributions": {
- "authorship": [
- "foellmelanie"
- ],
- "reviewing": [
- "bgruening",
- "simonbray",
- "foellmelanie",
- "bebatut",
- "shiltemann"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -403608,122 +367787,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
"twitter": "MCFoell",
"url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "simonbray",
- "joined": "2019-05",
- "name": "Simon Bray",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/metabolomics/tutorials/msi-finding-nglycans",
@@ -403739,7 +367802,6 @@
"id": "metabolomics/msi-finding-nglycans",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -403764,7 +367826,7 @@
"Preprocessing raw MSI data.",
"Performing supervised and unsupervised statistical analysis."
],
- "pageviews": 2499,
+ "pageviews": 2511,
"pub_date": "2019-04-13",
"questions": [
"Can N-linked glycans from FFPE tissues be detected by MALDI imaging?",
@@ -403782,18 +367844,18 @@
],
"short_id": "T00199",
"short_tools": [
- "Grep1",
- "cardinal_classification",
- "cardinal_mz_images",
- "cardinal_preprocessing",
+ "maldi_quant_peak_detection",
"Filter1",
- "cardinal_combine",
- "cardinal_segmentations",
+ "cardinal_quality_report",
+ "cardinal_preprocessing",
"maldi_quant_preprocessing",
+ "cardinal_mz_images",
+ "Grep1",
"join_files_on_column_fuzzy",
- "maldi_quant_peak_detection",
- "cardinal_quality_report",
- "Summary_Statistics1"
+ "cardinal_classification",
+ "cardinal_segmentations",
+ "Summary_Statistics1",
+ "cardinal_combine"
],
"slides": false,
"slides_recordings": false,
@@ -403816,11 +367878,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -403855,6 +367912,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -403910,10 +367971,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -403960,11 +368017,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -404009,6 +368061,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -404061,10 +368117,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -404105,10 +368157,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -404151,6 +368199,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -404203,10 +368255,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -404247,10 +368295,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -404293,6 +368337,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -404345,10 +368393,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -404389,10 +368433,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -404435,6 +368475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -404487,10 +368531,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -404534,11 +368574,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -404583,6 +368618,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -404635,10 +368674,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -404684,14 +368719,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -404738,6 +368765,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -404790,10 +368821,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -404839,14 +368866,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -404864,10 +368883,10 @@
"versions": [
"2.6.0.0",
"2.10.0.0",
- "3.4.3+galaxy0",
- "2.6.0.1",
"2.2.6.0",
- "2.4.0.1"
+ "2.6.0.1",
+ "2.4.0.1",
+ "3.4.3+galaxy0"
]
},
{
@@ -404900,6 +368919,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -404952,10 +368975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405001,14 +369020,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -405055,6 +369066,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -405107,10 +369122,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405156,15 +369167,6 @@
"state": "exact",
"version": "1.12.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.1",
- "3.4.3+galaxy0",
- "2.10.0.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -405211,6 +369213,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -405263,10 +369269,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405312,14 +369314,6 @@
"state": "exact",
"version": "1.12.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -405338,8 +369332,8 @@
"versions": [
"2.6.0.1",
"2.10.0.0",
- "1.12.1.4",
- "3.4.3+galaxy0"
+ "3.4.3+galaxy0",
+ "1.12.1.4"
]
},
{
@@ -405372,6 +369366,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -405424,10 +369422,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405473,14 +369467,6 @@
"state": "exact",
"version": "1.12.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -405527,6 +369513,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -405579,10 +369569,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405628,14 +369614,6 @@
"state": "exact",
"version": "1.18.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.22.0.0",
- "1.18.0.6"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -405652,8 +369630,8 @@
"state": "inexact",
"versions": [
"1.22.0.0",
- "1.18.0.5",
- "1.18.0.6"
+ "1.18.0.6",
+ "1.18.0.5"
]
},
{
@@ -405686,6 +369664,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -405738,10 +369720,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -405787,11 +369765,6 @@
"state": "exact",
"version": "1.18.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.18.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -405852,7 +369825,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 111,
- "visitors": 1716,
+ "visitors": 1724,
"workflows": [
{
"creators": [],
@@ -406011,7 +369984,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ntreated\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\ncontrol\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"MSI classification\"];\n 9 -->|outfile_imzml| 10;\n 4 -->|pixel_annotations| 10;\n 11[\"MSI segmentation\"];\n 9 -->|outfile_imzml| 11;\n 12[\"Filter\"];\n 10 -->|mzfeatures| 12;\n 13[\"Join two files\"];\n 12 -->|out_file1| 13;\n 2 -->|output| 13;\n 14[\"Summary Statistics\"];\n 13 -->|merged_file| 14;\n 15[\"MSI mz images\"];\n 13 -->|merged_file| 15;\n 3 -->|output| 15;\n 16[\"Select\"];\n 13 -->|merged_file| 16;\n 17[\"MSI mz images\"];\n 16 -->|out_file1| 17;\n 3 -->|output| 17;\n 2[\"\u2139\ufe0f Input Dataset\\nGlycan_IDs\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nall_files\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"MSI combine\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n 5[\"MSI preprocessing\"];\n 4 -->|outfile_imzml| 5;\n 6[\"MSI Qualitycontrol\"];\n 4 -->|outfile_imzml| 6;\n 4 -->|pixel_annotations| 6;\n 7[\"MALDIquant preprocessing\"];\n 5 -->|outfile_imzml| 7;\n 8[\"MALDIquant peak detection\"];\n 7 -->|outfile_imzml| 8;\n 4 -->|pixel_annotations| 8;\n 9[\"MSI preprocessing\"];\n 5 -->|outfile_imzml| 9;\n 8 -->|intensity_matrix| 9;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "MSI Finding Diff Analytes",
"outputs": [
{
@@ -407054,20 +371027,20 @@
],
"dir": "topics/metabolomics/tutorials/gc_ms_with_xcms",
"edam_operation": [
- "Imputation",
- "Chromatographic alignment",
"Clustering",
- "Correlation",
- "Chromatogram visualisation",
"Validation",
- "Mass spectrum visualisation",
- "Spectral library search",
+ "Filtering",
"Standardisation and normalisation",
- "Formatting",
"Label-free quantification",
+ "Chromatographic alignment",
+ "Format validation",
+ "Chromatogram visualisation",
+ "Imputation",
+ "Spectral library search",
+ "Formatting",
+ "Correlation",
"Peak detection",
- "Filtering",
- "Format validation"
+ "Mass spectrum visualisation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -407079,7 +371052,6 @@
"id": "metabolomics/gc_ms_with_xcms",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"js_requirements": {
@@ -407099,7 +371071,7 @@
"To explore what open-source alternative tools can be used in the analysis of GC-MS data, learn about their possible parametrisations.",
"To analyse authentic data samples and compare them with a data library of human metabolome, composed from a collection of mostly endogenous compounds."
],
- "pageviews": 2256,
+ "pageviews": 2280,
"pub_date": "2023-05-08",
"questions": [
"What are the main steps of gas chromatography-mass spectrometry (GC-MS) data processing for metabolomic analysis?",
@@ -407117,20 +371089,20 @@
],
"short_id": "T00344",
"short_tools": [
- "ramclustr",
+ "matchms_filtering",
+ "msnbase_readmsdata",
+ "waveica",
"matchms_similarity",
+ "abims_xcms_fillPeaks",
+ "matchms_formatter",
"ramclustr_define_experiment",
- "abims_xcms_retcor",
- "waveica",
- "msconvert",
- "matchms_filtering",
- "riassigner",
"abims_xcms_group",
- "abims_xcms_xcmsSet",
"xcms_merge",
- "abims_xcms_fillPeaks",
- "msnbase_readmsdata",
- "matchms_formatter"
+ "msconvert",
+ "abims_xcms_xcmsSet",
+ "riassigner",
+ "ramclustr",
+ "abims_xcms_retcor"
],
"slides": false,
"slides_recordings": false,
@@ -407148,11 +371120,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -407182,6 +371149,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -407237,10 +371208,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -407287,11 +371254,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -407336,6 +371298,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -407388,10 +371354,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -407424,8 +371386,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.19052.1",
- "3.0.19052.0"
+ "3.0.19052.0",
+ "3.0.19052.1"
]
},
{
@@ -407438,11 +371400,6 @@
"state": "exact",
"version": "3.0.20287.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.20287.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -407491,6 +371448,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -407543,10 +371504,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -407592,11 +371549,6 @@
"state": "exact",
"version": "2.16.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.16.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -407646,6 +371598,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -407698,10 +371654,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -407744,11 +371696,6 @@
"state": "exact",
"version": "3.12.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.12.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -407798,6 +371745,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -407850,10 +371801,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -407899,11 +371846,6 @@
"state": "exact",
"version": "3.12.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.12.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -407953,6 +371895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408005,10 +371951,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408054,11 +371996,6 @@
"state": "exact",
"version": "3.12.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.12.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -408108,6 +372045,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408160,10 +372101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408209,11 +372146,6 @@
"state": "exact",
"version": "3.12.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.12.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -408263,6 +372195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408315,10 +372251,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408364,11 +372296,6 @@
"state": "exact",
"version": "3.12.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.12.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -408418,6 +372345,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408470,10 +372401,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408518,11 +372445,6 @@
"state": "exact",
"version": "0.17.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.17.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -408536,8 +372458,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "0.20.0+galaxy0",
- "0.27.0+galaxy0"
+ "0.27.0+galaxy0",
+ "0.20.0+galaxy0"
]
},
{
@@ -408570,6 +372492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408622,10 +372548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408670,11 +372592,6 @@
"state": "exact",
"version": "0.20.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -408683,8 +372600,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "0.27.0+galaxy0",
"0.25.0+galaxy0",
+ "0.27.0+galaxy0",
"0.1.4"
]
},
@@ -408723,6 +372640,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408775,10 +372696,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408823,13 +372740,6 @@
"state": "exact",
"version": "0.20.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.22.0+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -408873,6 +372783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -408925,10 +372839,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -408973,11 +372883,6 @@
"state": "exact",
"version": "1.2.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.4+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -408991,8 +372896,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.3.0+galaxy7",
- "1.3.0+galaxy1"
+ "1.3.0+galaxy1",
+ "1.3.0+galaxy7"
]
},
{
@@ -409025,6 +372930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -409077,10 +372986,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -409125,11 +373030,6 @@
"state": "exact",
"version": "1.3.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -409146,8 +373046,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.3.0+galaxy7",
- "1.3.0+galaxy1"
+ "1.3.0+galaxy1",
+ "1.3.0+galaxy7"
]
},
{
@@ -409180,6 +373080,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -409232,10 +373136,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -409280,13 +373180,6 @@
"state": "exact",
"version": "1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.2+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -409334,6 +373227,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -409386,10 +373283,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -409432,11 +373325,6 @@
"state": "exact",
"version": "0.3.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -409483,6 +373371,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -409535,10 +373427,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -409583,17 +373471,6 @@
"state": "exact",
"version": "0.2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.2.0+galaxy4",
- "0.2.0+galaxy7",
- "0.2.0+galaxy5",
- "0.2.0+galaxy6",
- "0.2.0+galaxy8"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -409659,7 +373536,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 97,
- "visitors": 1701,
+ "visitors": 1720,
"workflows": [
{
"creators": [
@@ -409846,7 +373723,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference spectra\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"msconvert\"];\n 3 -->|output| 4;\n 5[\"MSnbase readMSData\"];\n 4 -->|output| 5;\n 6[\"xcms findChromPeaks xcmsSet\"];\n 5 -->|xsetRData| 6;\n 7[\"xcms findChromPeaks Merger\"];\n 6 -->|xsetRData| 7;\n 2 -->|output| 7;\n 8[\"xcms groupChromPeaks group\"];\n 7 -->|xsetRData| 8;\n 9[\"xcms adjustRtime retcor\"];\n 8 -->|xsetRData| 9;\n 10[\"xcms groupChromPeaks group\"];\n 9 -->|xsetRData| 10;\n 11[\"xcms fillChromPeaks fillPeaks\"];\n 10 -->|xsetRData| 11;\n 940c7549-1bae-4ddd-9e92-75fc7d2c8eef[\"Output\\nFeature (peak) intensities\"];\n 11 --> 940c7549-1bae-4ddd-9e92-75fc7d2c8eef;\n style 940c7549-1bae-4ddd-9e92-75fc7d2c8eef stroke:#2c3143,stroke-width:4px;\n 9f910e82-e7a5-4201-b944-1845ba6aa2e9[\"Output\\nFeature (peak) metadata (mz, rt, ...)\"];\n 11 --> 9f910e82-e7a5-4201-b944-1845ba6aa2e9;\n style 9f910e82-e7a5-4201-b944-1845ba6aa2e9 stroke:#2c3143,stroke-width:4px;\n 5bab8f28-4df1-4397-af04-168546bd0e52[\"Output\\nxcmsObj (XCMSnExp)\"];\n 11 --> 5bab8f28-4df1-4397-af04-168546bd0e52;\n style 5bab8f28-4df1-4397-af04-168546bd0e52 stroke:#2c3143,stroke-width:4px;\n 12[\"RAMClustR\"];\n 11 -->|xsetRData| 12;\n 92fac5e6-1578-4e52-ac9d-2982e19a5b88[\"Output\\nDeconvoluted spectra\"];\n 12 --> 92fac5e6-1578-4e52-ac9d-2982e19a5b88;\n style 92fac5e6-1578-4e52-ac9d-2982e19a5b88 stroke:#2c3143,stroke-width:4px;\n f7657c17-6293-4fbb-b014-28009d495de7[\"Output\\nFeature (spectra) intensities\"];\n 12 --> f7657c17-6293-4fbb-b014-28009d495de7;\n style f7657c17-6293-4fbb-b014-28009d495de7 stroke:#2c3143,stroke-width:4px;\n 13[\"RIAssigner\"];\n 12 -->|mass_spectra_merged| 13;\n 0 -->|output| 13;\n 7ec6ce02-5d83-48ab-ba0a-94976db297e5[\"Output\\nRetention indexed spectra\"];\n 13 --> 7ec6ce02-5d83-48ab-ba0a-94976db297e5;\n style 7ec6ce02-5d83-48ab-ba0a-94976db297e5 stroke:#2c3143,stroke-width:4px;\n 14[\"matchms similarity\"];\n 13 -->|output| 14;\n 1 -->|output| 14;\n 024327f7-13b8-4ce9-8708-9f430d7ceedf[\"Output\\nCosineGreedy scores of input dataset(s)\"];\n 14 --> 024327f7-13b8-4ce9-8708-9f430d7ceedf;\n style 024327f7-13b8-4ce9-8708-9f430d7ceedf stroke:#2c3143,stroke-width:4px;\n 15[\"matchms scores formatter\"];\n 14 -->|similarity_scores| 15;\n 8a767006-4b3c-41ba-bea5-18fd100ce930[\"Output\\nmatchms_scores\"];\n 15 --> 8a767006-4b3c-41ba-bea5-18fd100ce930;\n style 8a767006-4b3c-41ba-bea5-18fd100ce930 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GC MS using XCMS",
"outputs": [
{
@@ -410594,7 +374471,6 @@
"inexact_supported_servers": [
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -410618,7 +374494,7 @@
"Automatic generation of many m/z images.",
"Overlay the distribution of several m/z in one image."
],
- "pageviews": 3776,
+ "pageviews": 3789,
"pub_date": "2019-02-21",
"questions": [
"What is the typical mass range of VOCs?",
@@ -410627,12 +374503,12 @@
],
"short_id": "T00198",
"short_tools": [
- "cardinal_mz_images",
- "Filter1",
- "cardinal_spectra_plots",
- "cardinal_data_exporter",
"cardinal_filtering",
- "cardinal_quality_report"
+ "cardinal_spectra_plots",
+ "Filter1",
+ "cardinal_quality_report",
+ "cardinal_mz_images",
+ "cardinal_data_exporter"
],
"slides": false,
"slides_recordings": false,
@@ -410655,11 +374531,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -410694,6 +374565,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -410749,10 +374624,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -410799,11 +374670,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -410848,6 +374714,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -410900,10 +374770,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -410944,10 +374810,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -410990,6 +374852,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411042,10 +374908,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411091,14 +374953,6 @@
"state": "exact",
"version": "2.6.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411145,6 +374999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411197,10 +375055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411246,14 +375100,6 @@
"state": "exact",
"version": "2.6.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411300,6 +375146,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411352,10 +375202,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411388,8 +375234,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12.1.2",
- "2.6.0.1"
+ "2.6.0.1",
+ "1.12.1.2"
]
},
{
@@ -411404,14 +375250,6 @@
"state": "exact",
"version": "2.6.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411427,12 +375265,12 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.12.1.2",
"2.6.0.1",
+ "1.12.1.2",
"2.10.0.0",
"2.6.0.2",
- "2.4.0.0",
- "3.4.3+galaxy0"
+ "3.4.3+galaxy0",
+ "2.4.0.0"
]
},
{
@@ -411465,6 +375303,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411517,10 +375359,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411553,8 +375391,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12.1.2",
- "2.6.0.1"
+ "2.6.0.1",
+ "1.12.1.2"
]
},
{
@@ -411569,14 +375407,6 @@
"state": "exact",
"version": "2.6.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411623,6 +375453,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411675,10 +375509,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411724,14 +375554,6 @@
"state": "exact",
"version": "2.6.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411779,6 +375601,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411831,10 +375657,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -411880,14 +375702,6 @@
"state": "exact",
"version": "2.6.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -411905,10 +375719,10 @@
"versions": [
"2.6.0.1",
"2.10.0.0",
- "2.6.0.3",
"3.4.3+galaxy0",
+ "1.12.1.3",
"2.6.0.2",
- "1.12.1.3"
+ "2.6.0.3"
]
},
{
@@ -411941,6 +375755,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -411993,10 +375811,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -412029,8 +375843,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.6.0.0",
- "2.6.0.1"
+ "2.6.0.1",
+ "2.6.0.0"
]
},
{
@@ -412045,14 +375859,6 @@
"state": "exact",
"version": "2.6.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.10.0.0",
- "3.4.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -412111,7 +375917,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 104,
- "visitors": 2606,
+ "visitors": 2614,
"workflows": [
{
"creators": [],
@@ -412250,7 +376056,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nUploaded Composite Dataset imzml\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nAnnotation\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nm/z features\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"MSI Qualitycontrol\"];\n 0 -->|output| 3;\n 4[\"MSI plot spectra\"];\n 0 -->|output| 4;\n 5[\"MSI filtering\"];\n 0 -->|output| 5;\n 6[\"MSI plot spectra\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 7[\"MSI data exporter\"];\n 5 -->|outfile_imzml| 7;\n 8[\"MSI mz images\"];\n 2 -->|output| 8;\n 5 -->|outfile_imzml| 8;\n 9[\"Filter\"];\n 7 -->|feature_output| 9;\n 10[\"MSI mz images\"];\n 9 -->|out_file1| 10;\n 5 -->|outfile_imzml| 10;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "MSI Workflow: spatial distribution",
"outputs": [
{
@@ -413077,7 +376883,7 @@
"To generate 3D conformers and optimise them using semi-empirical quantum mechanical (SQM) methods.",
"To produce simulated mass spectra for a given molecule in MSP (text based) format."
],
- "pageviews": 289851,
+ "pageviews": 312678,
"pub_date": "2024-10-01",
"questions": [
"Can I predict QC-based mass spectra starting from SMILES?",
@@ -413096,17 +376902,17 @@
],
"short_id": "T00458",
"short_tools": [
+ "__FILTER_FAILED_DATASETS__",
"openbabel_compound_convert",
- "tp_cut_tool",
+ "xtb_molecular_optimization",
+ "qcxms_neutral_run",
"tp_cat",
- "qcxms_production_run",
"split_file_to_collection",
+ "qcxms_production_run",
"ctb_im_conformers",
- "qcxms_neutral_run",
+ "tp_cut_tool",
"param_value_from_file",
- "qcxms_getres",
- "__FILTER_FAILED_DATASETS__",
- "xtb_molecular_optimization"
+ "qcxms_getres"
],
"slides": true,
"slides_recordings": false,
@@ -413148,6 +376954,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -413203,10 +377013,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -413253,11 +377059,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -413302,6 +377103,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -413354,10 +377159,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -413398,10 +377199,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -413444,6 +377241,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -413496,10 +377297,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -413540,10 +377337,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -413586,6 +377379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -413638,10 +377435,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -413684,10 +377477,6 @@
"state": "exact",
"version": "1.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -413733,6 +377522,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -413786,10 +377579,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -413835,10 +377624,6 @@
"state": "exact",
"version": "3.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -413884,6 +377669,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -413916,8 +377705,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.4.0",
- "0.5.1"
+ "0.5.1",
+ "0.4.0"
]
},
{
@@ -413940,10 +377729,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -413987,8 +377772,8 @@
"versions": [
"0.4.0",
"0.2.0",
- "0.1.1",
- "0.5.0"
+ "0.5.0",
+ "0.1.1"
]
},
{
@@ -413996,11 +377781,6 @@
"state": "exact",
"version": "0.5.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -414049,6 +377829,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414073,8 +377857,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -414085,8 +377869,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -414109,10 +377893,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -414153,8 +377933,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -414162,17 +377942,12 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -414215,6 +377990,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414273,10 +378052,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -414326,11 +378101,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -414378,6 +378148,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414430,10 +378204,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -414475,10 +378245,6 @@
"state": "exact",
"version": "5.2.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -414522,6 +378288,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414574,10 +378344,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -414619,10 +378385,6 @@
"state": "exact",
"version": "5.2.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -414669,6 +378431,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414721,10 +378487,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -414766,10 +378528,6 @@
"state": "exact",
"version": "5.2.1+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -414813,6 +378571,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -414865,10 +378627,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -414910,10 +378668,6 @@
"state": "exact",
"version": "5.2.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -414957,6 +378711,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -415009,10 +378767,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -415054,11 +378808,6 @@
"state": "exact",
"version": "6.6.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "6.6.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -415104,6 +378853,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -415156,10 +378909,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -415201,11 +378950,6 @@
"state": "exact",
"version": "6.6.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "6.6.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -415265,8 +379009,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 254,
- "visitors": 110611,
+ "visit_duration": 248,
+ "visitors": 120352,
"workflows": [
{
"creators": [
@@ -415407,7 +379151,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput Molecules with SMILES and NAME without a header.\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nNumber of conformers to generate\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nOptimization Levels\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nQC Method\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"Cut SMILES column\"];\n 0 -->|output| 4;\n 5[\"Cut NAME column\"];\n 0 -->|output| 5;\n 6[\"Split file\"];\n 4 -->|output| 6;\n 7[\"Split file\"];\n 5 -->|output| 7;\n 8[\"Parse parameter value\"];\n 7 -->|list_output_tab| 8;\n 9[\"Convert compounds from SMILES to SDF and add the name as title.\"];\n 8 -->|text_param| 9;\n 6 -->|list_output_tab| 9;\n 10[\"Merge the individual SDF files\"];\n 9 -->|outfile| 10;\n 11[\"Generate conformers\"];\n 10 -->|out_file1| 11;\n 1 -->|output| 11;\n f4f8881e-cd64-42ae-8435-1288e4e473b5[\"Output\\nconformer_output\"];\n 11 --> f4f8881e-cd64-42ae-8435-1288e4e473b5;\n style f4f8881e-cd64-42ae-8435-1288e4e473b5 stroke:#2c3143,stroke-width:4px;\n 12[\"Molecular format conversion \"];\n 11 -->|outfile| 12;\n 5dcb6f02-62c9-4f43-9810-a10052b59b41[\"Output\\nXYZ output\"];\n 12 --> 5dcb6f02-62c9-4f43-9810-a10052b59b41;\n style 5dcb6f02-62c9-4f43-9810-a10052b59b41 stroke:#2c3143,stroke-width:4px;\n 13[\"xTB molecular optimization\"];\n 12 -->|file_outputs| 13;\n 2 -->|output| 13;\n 01a9a1af-e225-4613-94f9-dfdad37c93a2[\"Output\\noptimized output\"];\n 13 --> 01a9a1af-e225-4613-94f9-dfdad37c93a2;\n style 01a9a1af-e225-4613-94f9-dfdad37c93a2 stroke:#2c3143,stroke-width:4px;\n 14[\"QCxMS neutral run\"];\n 3 -->|output| 14;\n 13 -->|output| 14;\n e6e6a07b-d478-4a87-b491-42abee9094b1[\"Output\\n[.in] output\"];\n 14 --> e6e6a07b-d478-4a87-b491-42abee9094b1;\n style e6e6a07b-d478-4a87-b491-42abee9094b1 stroke:#2c3143,stroke-width:4px;\n 969b3e2f-fbee-48f9-829a-c0032580e6f8[\"Output\\n[.xyz] output\"];\n 14 --> 969b3e2f-fbee-48f9-829a-c0032580e6f8;\n style 969b3e2f-fbee-48f9-829a-c0032580e6f8 stroke:#2c3143,stroke-width:4px;\n dc4811ad-6cff-42cc-a2f8-52ab585f47fe[\"Output\\n[.start] output\"];\n 14 --> dc4811ad-6cff-42cc-a2f8-52ab585f47fe;\n style dc4811ad-6cff-42cc-a2f8-52ab585f47fe stroke:#2c3143,stroke-width:4px;\n 15[\"QCxMS production run\"];\n 14 -->|coords1| 15;\n 14 -->|coords2| 15;\n 14 -->|coords3| 15;\n fc53168a-99f8-441c-9325-2d812bf03100[\"Output\\nres output\"];\n 15 --> fc53168a-99f8-441c-9325-2d812bf03100;\n style fc53168a-99f8-441c-9325-2d812bf03100 stroke:#2c3143,stroke-width:4px;\n 16[\"Filter failed datasets\"];\n 15 -->|res_files| 16;\n 17[\"QCxMS get results\"];\n 12 -->|file_outputs| 17;\n 16 -->|output| 17;\n d81bf92a-604c-46b9-86a9-bf3c2281ebcb[\"Output\\nMSP output\"];\n 17 --> d81bf92a-604c-46b9-86a9-bf3c2281ebcb;\n style d81bf92a-604c-46b9-86a9-bf3c2281ebcb stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "End-to-end EI+ mass spectra prediction workflow using QCxMS",
"outputs": [
{
@@ -416131,12 +379875,12 @@
],
"dir": "topics/metabolomics/tutorials/lcms",
"edam_operation": [
+ "Validation",
+ "Label-free quantification",
+ "Filtering",
"Chromatographic alignment",
"Chromatogram visualisation",
- "Label-free quantification",
"Peak detection",
- "Validation",
- "Filtering",
"Mass spectrum visualisation"
],
"edam_topic": [],
@@ -416148,7 +379892,6 @@
"inexact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -416169,7 +379912,7 @@
"To get familiar with the main steps constituting a metabolomic workflow for untargeted LC-MS analysis.",
"To evaluate the potential of a workflow approach when dealing with LC-MS metabolomic data."
],
- "pageviews": 18641,
+ "pageviews": 18676,
"pub_date": "2019-07-02",
"questions": [
"What are the main steps of untargeted LC-MS data processing for metabolomic analysis?",
@@ -416177,19 +379920,19 @@
],
"short_id": "T00195",
"short_tools": [
- "Batch_correction",
+ "msnbase_readmsdata",
+ "quality_metrics",
+ "abims_CAMERA_annotateDiffreport",
"abims_xcms_fillPeaks",
- "abims_xcms_retcor",
"abims_xcms_group",
- "xcms_plot_chromatogram",
- "quality_metrics",
- "abims_xcms_xcmsSet",
"xcms_merge",
- "wsdl_hmdb",
+ "abims_xcms_retcor",
"generic_filter",
- "Univariate",
- "msnbase_readmsdata",
- "abims_CAMERA_annotateDiffreport"
+ "abims_xcms_xcmsSet",
+ "xcms_plot_chromatogram",
+ "Batch_correction",
+ "wsdl_hmdb",
+ "Univariate"
],
"slides": false,
"slides_recordings": false,
@@ -416206,11 +379949,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -416245,6 +379983,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -416300,10 +380042,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -416350,11 +380088,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -416399,6 +380132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -416451,10 +380188,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -416498,11 +380231,6 @@
"state": "exact",
"version": "2.2.8"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.8"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -416547,6 +380275,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -416600,10 +380332,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -416647,11 +380375,6 @@
"state": "exact",
"version": "2.2.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -416697,6 +380420,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -416749,10 +380476,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -416803,14 +380526,6 @@
"1.7.6"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.7.6",
- "1.7.4"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -416859,6 +380574,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -416911,10 +380630,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -416958,11 +380673,6 @@
"state": "exact",
"version": "2.2.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417012,6 +380722,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417064,10 +380778,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417111,11 +380821,6 @@
"state": "exact",
"version": "2.8.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.8.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417164,6 +380869,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417216,10 +380925,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417262,11 +380967,6 @@
"state": "exact",
"version": "3.4.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417315,6 +381015,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417367,10 +381071,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417408,8 +381108,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.12.0+galaxy0",
- "2.1.0"
+ "2.1.0",
+ "3.12.0+galaxy0"
]
},
{
@@ -417417,11 +381117,6 @@
"state": "exact",
"version": "3.4.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417470,6 +381165,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417522,10 +381221,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417569,11 +381264,6 @@
"state": "exact",
"version": "3.4.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417622,6 +381312,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417674,10 +381368,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417721,11 +381411,6 @@
"state": "exact",
"version": "3.4.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417774,6 +381459,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417826,10 +381515,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -417873,11 +381558,6 @@
"state": "exact",
"version": "3.4.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -417926,6 +381606,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -417978,10 +381662,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -418025,11 +381705,6 @@
"state": "exact",
"version": "3.4.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -418078,6 +381753,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -418130,10 +381809,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -418177,11 +381852,6 @@
"state": "exact",
"version": "2.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -418226,6 +381896,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -418278,10 +381952,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -418325,14 +381995,6 @@
"state": "exact",
"version": "2017.04"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2017.06",
- "2020.01"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -418398,7 +382060,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 95,
- "visitors": 11085,
+ "visitors": 11112,
"workflows": [
{
"creators": [],
@@ -418496,7 +382158,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"xcms fillChromPeaks fillPeaks\"];\n 9 -->|xsetRData| 10;\n 11[\"CAMERA.annotate\"];\n 10 -->|xsetRData| 11;\n 12[\"Batch_correction\"];\n 10 -->|dataMatrix| 12;\n 0 -->|output| 12;\n 11 -->|variableMetadata| 12;\n 13[\"Quality Metrics\"];\n 10 -->|dataMatrix| 13;\n 0 -->|output| 13;\n 11 -->|variableMetadata| 13;\n 14[\"Quality Metrics\"];\n 12 -->|dataMatrix_out| 14;\n 0 -->|output| 14;\n 12 -->|variableMetadata_out| 14;\n 15[\"Generic_Filter\"];\n 12 -->|dataMatrix_out| 15;\n 14 -->|sampleMetadata_out| 15;\n 14 -->|variableMetadata_out| 15;\n 16[\"Univariate\"];\n 15 -->|dataMatrix_out| 16;\n 15 -->|sampleMetadata_out| 16;\n 15 -->|variableMetadata_out| 16;\n 17[\"Generic_Filter\"];\n 15 -->|dataMatrix_out| 17;\n 15 -->|sampleMetadata_out| 17;\n 16 -->|variableMetadata_out| 17;\n 18[\"HMDB MS search\"];\n 17 -->|variableMetadata_out| 18;\n 2[\"MSnbase readMSData\"];\n 1 -->|output| 2;\n 3[\"xcms findChromPeaks xcmsSet\"];\n 2 -->|xsetRData| 3;\n 4[\"xcms plot chromatogram\"];\n 3 -->|xsetRData| 4;\n 5[\"xcms findChromPeaks Merger\"];\n 3 -->|xsetRData| 5;\n 6[\"xcms groupChromPeaks group\"];\n 5 -->|xsetRData| 6;\n 7[\"xcms adjustRtime retcor\"];\n 6 -->|xsetRData| 7;\n 8[\"xcms plot chromatogram\"];\n 7 -->|xsetRData| 8;\n 9[\"xcms groupChromPeaks group\"];\n 7 -->|xsetRData| 9;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Workflow Constructed From History 'imported: testpourGCC'",
"outputs": [],
"parent_id": "metabolomics/lcms",
@@ -418637,13 +382299,9 @@
"lecorguille",
"workflow4metabolomics"
],
- "reviewing": [
- "hexylena",
- "shiltemann",
- "melpetera",
- "lecorguille",
- "foellmelanie",
- "bgruening"
+ "editing": [],
+ "funding": [
+ "elixir-europe"
]
},
"contributors": [
@@ -418678,146 +382336,20 @@
"name": "Workflow4Metabolomics core team",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/workflow4metabolomics/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
- },
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
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- "name": "Helena Rasche",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- {
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- "elixir-europe"
- ],
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- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
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- "joined": "2019-06",
- "name": "M\u00e9lanie Petera",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
- },
- {
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- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
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- "twitter": "MCFoell",
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- "deNBI",
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/metabolomics/tutorials/lcms-preprocessing",
"edam_operation": [
+ "Validation",
+ "Label-free quantification",
+ "Filtering",
"Chromatographic alignment",
"Chromatogram visualisation",
- "Label-free quantification",
"Peak detection",
- "Validation",
- "Filtering",
"Mass spectrum visualisation"
],
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"exact_supported_servers": [
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -418847,7 +382379,7 @@
"To get familiar with the way to use XCMS-based Galaxy modules dedicated to LC-MS data preprocessing.",
"To evaluate the potential of a workflow approach when dealing with LC-MS preprocessing."
],
- "pageviews": 6187698,
+ "pageviews": 6210532,
"pub_date": "2020-02-04",
"questions": [
"What are the main steps of untargeted LC-MS data preprocessing for metabolomic analyses?",
@@ -418855,28 +382387,23 @@
],
"short_id": "T00197",
"short_tools": [
+ "msnbase_readmsdata",
+ "abims_xcms_fillPeaks",
+ "abims_CAMERA_annotateDiffreport",
"idchoice",
- "abims_xcms_retcor",
"intens_check",
"abims_xcms_group",
+ "xcms_merge",
+ "abims_xcms_xcmsSet",
"xcms_plot_chromatogram",
"abims_xcms_summary",
- "abims_xcms_xcmsSet",
- "xcms_merge",
"xcms_export_samplemetadata",
- "abims_xcms_fillPeaks",
- "msnbase_readmsdata",
- "abims_CAMERA_annotateDiffreport"
+ "abims_xcms_retcor"
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"url": "https://usegalaxy.org",
@@ -418923,6 +382450,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -418978,10 +382509,6 @@
"name": "InteractoMIX",
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},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
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@@ -419028,11 +382555,6 @@
"url": "https://usegalaxy.eu",
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},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -419077,6 +382599,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "missing"
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@@ -419182,16 +382704,11 @@
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"2.2.0",
+ "2.2.2",
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- "2.2.1",
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+ "2.2.1"
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"state": "inexact",
@@ -419241,6 +382758,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"state": "inexact",
@@ -419396,6 +382908,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"3.12.0+galaxy1"
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"state": "inexact",
@@ -419553,6 +383060,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
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{
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@@ -419705,6 +383207,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
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{
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- "state": "exact",
- "version": "3.12.0+galaxy0"
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{
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"state": "inexact",
@@ -419860,6 +383357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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{
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"state": "inexact",
@@ -420015,6 +383507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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{
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"state": "inexact",
@@ -420170,6 +383657,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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@@ -420222,10 +383713,6 @@
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@@ -420271,11 +383758,6 @@
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{
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"state": "inexact",
@@ -420325,6 +383807,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -420377,10 +383863,6 @@
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{
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@@ -420423,11 +383905,6 @@
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},
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- "version": "3.12.0+galaxy0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -420477,6 +383954,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -420529,10 +384010,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -420578,11 +384055,6 @@
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},
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- "state": "exact",
- "version": "3.12.0+galaxy0"
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{
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"state": "inexact",
@@ -420632,6 +384104,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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@@ -420684,10 +384160,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
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@@ -420732,11 +384204,6 @@
"state": "exact",
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- "version": "19.12"
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{
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"state": "inexact",
@@ -420783,6 +384250,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -420835,10 +384306,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
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{
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@@ -420886,11 +384353,6 @@
"1.3.0"
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{
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@@ -420952,8 +384414,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 294,
- "visitors": 2247776,
+ "visit_duration": 293,
+ "visitors": 2258501,
"zenodo_link": "https://zenodo.org/record/3757956"
},
{
@@ -420965,22 +384427,6 @@
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- "shiltemann",
- "RJMW",
- "lecorguille",
- "hexylena"
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@@ -421000,150 +384446,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/cecilecanlet/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/cecilecanlet.json"
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- "elixir-europe"
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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@@ -421168,7 +384470,7 @@
"license": "CC-BY-4.0",
"logo": "GTN",
"mod_date": "2023-01-12",
- "pageviews": 6179322,
+ "pageviews": 6202126,
"priority": 1,
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"redirect_from": [
@@ -421240,7 +384542,7 @@
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"video_view": 0,
"visit_duration": 153,
- "visitors": 2242621
+ "visitors": 2253323
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@@ -421287,17 +384589,6 @@
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"draft": true,
"edam_operation": [
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+ "Label-free quantification",
+ "Filtering",
"Chromatographic alignment",
"Chromatogram visualisation",
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- "Filtering",
"Mass spectrum visualisation"
],
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@@ -421411,7 +384641,7 @@
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@@ -421428,11 +384658,11 @@
],
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"short_tools": [
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+ "abims_xcms_fillPeaks",
"abims_xcms_group",
- "abims_xcms_xcmsSet",
"xcms_merge",
- "abims_xcms_fillPeaks",
- "msnbase_readmsdata"
+ "abims_xcms_xcmsSet"
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"slides_recordings": false,
@@ -421448,11 +384678,6 @@
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{
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"url": "https://usegalaxy.org",
@@ -421494,6 +384719,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -421549,10 +384778,6 @@
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"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -421599,11 +384824,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -421648,6 +384868,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -421700,10 +384924,6 @@
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@@ -421749,11 +384969,6 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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+ "state": "missing"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
"servers": [
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@@ -424147,7 +387126,7 @@
"license": "CC-BY-4.0",
"logo": "GTN",
"mod_date": "2024-08-08",
- "pageviews": 6179322,
+ "pageviews": 6202126,
"priority": 0,
"pub_date": "2017-06-22",
"recordings": [
@@ -424250,7 +387229,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 153,
- "visitors": 2242621
+ "visitors": 2253323
},
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@@ -424409,23 +387388,6 @@
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@@ -424673,13 +387458,13 @@
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],
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- "Visualisation",
"Phylogenetic analysis",
+ "Visualisation",
+ "Sequence clustering",
+ "DNA barcoding",
"Sequencing quality control",
"Taxonomic classification",
- "Sequence read processing",
- "DNA barcoding"
+ "Sequence read processing"
],
"edam_topic": [
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@@ -424694,7 +387479,6 @@
"hands_on": true,
"id": "microbiome/general-tutorial",
"inexact_supported_servers": [
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"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -424716,7 +387500,7 @@
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"Visualisation of a community structure"
],
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+ "pageviews": 6182,
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"questions": [
"How to analyze metagenomics data?",
@@ -424732,27 +387516,27 @@
],
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+ "humann2_renorm_table",
"metaphlan2krona",
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- "mothur_cluster_split",
- "mothur_merge_files",
- "mothur_make_group",
- "metaphlan2",
"mothur_filter_seqs",
+ "mothur_make_group",
+ "taxonomy_krona_chart",
"mothur_screen_seqs",
"mothur_classify_otu",
+ "mothur_align_seqs",
+ "mothur_summary_seqs",
+ "mothur_unique_seqs",
"mothur_count_seqs",
"krona-text",
- "taxonomy_krona_chart",
+ "humann2",
+ "mothur_cluster_split",
+ "mothur_make_biom",
"mothur_classify_seqs",
- "mothur_align_seqs",
+ "humann2_regroup_table",
"mothur_make_shared",
- "mothur_unique_seqs",
"mothur_pre_cluster",
- "mothur_summary_seqs",
- "humann2_renorm_table",
- "humann2"
+ "mothur_merge_files",
+ "metaphlan2"
],
"slides": false,
"slides_recordings": false,
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -424799,6 +387578,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
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"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -424953,6 +387727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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- "2.7.1"
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{
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"state": "inexact",
@@ -425123,6 +387889,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -425155,8 +387925,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
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- "0.11.1.0"
+ "0.11.1.0",
+ "0.11.1.3"
]
},
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"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.eu",
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{
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"state": "inexact",
"versions": [
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"0.11.1.0",
+ "0.11.1.3",
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]
},
@@ -425285,6 +388043,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"state": "inexact",
@@ -425444,6 +388194,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "inexact",
@@ -425603,6 +388345,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -425659,10 +388405,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -425704,11 +388446,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "inexact",
@@ -425757,6 +388494,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -425811,10 +388552,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
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@@ -425858,11 +388595,6 @@
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{
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@@ -425908,163 +388640,7 @@
"state": "missing"
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- "server": "https://usegalaxy.fr/",
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- "state": "missing"
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- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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},
{
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"server": "http://galaxy.interactomix.com/",
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- {
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- "state": "missing"
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{
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@@ -426172,12 +388744,158 @@
"version": "1.36.1.0"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.39.5.0"
]
},
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.36.1.0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "inexact",
+ "versions": [
+ "1.39.5.0"
+ ]
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
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+ "version": "1.36.1.0"
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "inexact",
+ "versions": [
+ "1.39.5.0"
+ ]
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
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+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
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+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.36.1.0"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
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+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.36.1.0"
+ },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -426227,6 +388945,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -426282,10 +389004,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -426331,13 +389049,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -426387,6 +389098,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -426442,10 +389157,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -426491,13 +389202,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -426547,6 +389251,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -426602,10 +389310,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -426651,13 +389355,6 @@
"state": "exact",
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},
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- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -426707,6 +389404,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -426762,10 +389463,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -426811,13 +389508,6 @@
"state": "exact",
"version": "1.36.1.0"
},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -426867,6 +389557,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -426922,10 +389616,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -426971,13 +389661,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -427027,6 +389710,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -427082,10 +389769,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -427131,13 +389814,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
- },
{
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"state": "inexact",
@@ -427187,6 +389863,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -427242,10 +389922,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -427291,13 +389967,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
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{
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"state": "inexact",
@@ -427347,6 +390016,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -427402,10 +390075,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -427451,13 +390120,6 @@
"state": "exact",
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},
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- "versions": [
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- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -427507,6 +390169,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -427562,10 +390228,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
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@@ -427611,13 +390273,6 @@
"state": "exact",
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- ]
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{
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"state": "inexact",
@@ -427667,6 +390322,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -427722,10 +390381,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -427771,14 +390426,6 @@
"state": "exact",
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- "server": "https://usegalaxy.fr/",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -427830,6 +390477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -427885,10 +390536,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
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@@ -427934,13 +390581,6 @@
"state": "exact",
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},
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{
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"state": "inexact",
@@ -427990,6 +390630,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -428045,10 +390689,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -428094,13 +390734,6 @@
"state": "exact",
"version": "1.36.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.39.5.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -428150,6 +390783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -428203,10 +390840,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -428250,11 +390883,6 @@
"state": "exact",
"version": "1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -428327,8 +390955,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 177,
- "visitors": 4472,
+ "visit_duration": 176,
+ "visitors": 4530,
"workflows": [
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@@ -428339,7 +390967,7 @@
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"hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -428482,8 +391110,8 @@
}
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Merge.files\"];\n 2 -->|output| 5;\n 1 -->|output| 5;\n 6[\"Make.group\"];\n 1 -->|output| 6;\n 2 -->|output| 6;\n 7[\"Unique.seqs\"];\n 5 -->|output| 7;\n 8[\"Count.seqs\"];\n 6 -->|output| 8;\n 7 -->|out_names| 8;\n 9[\"Summary.seqs\"];\n 8 -->|seq_count| 9;\n 7 -->|out_fasta| 9;\n 10[\"Screen.seqs\"];\n 7 -->|out_fasta| 10;\n 8 -->|seq_count| 10;\n 11[\"Align.seqs\"];\n 0 -->|output| 11;\n 10 -->|fasta_out| 11;\n 12[\"Summary.seqs\"];\n 10 -->|count_out| 12;\n 11 -->|out_file| 12;\n 13[\"Screen.seqs\"];\n 11 -->|out_file| 13;\n 10 -->|count_out| 13;\n 14[\"Filter.seqs\"];\n 13 -->|fasta_out| 14;\n 15[\"Pre.cluster\"];\n 14 -->|filteredfasta| 15;\n 13 -->|count_out| 15;\n 16[\"Classify.seqs\"];\n 15 -->|count_out| 16;\n 3 -->|output| 16;\n 15 -->|fasta_out| 16;\n 4 -->|output| 16;\n 17[\"Cluster.split\"];\n 16 -->|taxonomy_out| 17;\n 15 -->|fasta_out| 17;\n 15 -->|count_out| 17;\n 18[\"Make.shared\"];\n 15 -->|count_out| 18;\n 17 -->|otulist| 18;\n 5c0f4ca0-eb86-4361-8d87-f54baeee8345[\"Output\\nmothur_make_shared_shared\"];\n 18 --> 5c0f4ca0-eb86-4361-8d87-f54baeee8345;\n style 5c0f4ca0-eb86-4361-8d87-f54baeee8345 stroke:#2c3143,stroke-width:4px;\n 19[\"Classify.otu\"];\n 15 -->|count_out| 19;\n 16 -->|taxonomy_out| 19;\n 17 -->|otulist| 19;\n 20[\"Make.biom\"];\n 18 -->|shared| 20;\n 19 -->|taxonomies| 20;\n 21[\"Visualize with Krona\"];\n 19 -->|taxonomies| 21;",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Amplicon Tutorial",
"outputs": [
{
@@ -428551,7 +391179,7 @@
{
"label": "mothur_make_shared_shared",
"output_name": "shared",
- "uuid": "b3290d84-3cc4-4111-9d45-9ed82bb4ec76"
+ "uuid": "5c0f4ca0-eb86-4361-8d87-f54baeee8345"
}
]
}
@@ -428641,7 +391269,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
"outputs": [],
"parent_id": "microbiome/general-tutorial",
@@ -428810,24 +391438,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: combine_metaphlan2_humann2\n owner: bebatut\n revisions: fdfb35745104\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n owner: crs4\n revisions: e9005d1f3cfd\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_paired_end_interlacer\n owner: devteam\n revisions: 2ccb8dcabddc\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: export2graphlan\n owner: iuc\n revisions: 635c90a27692\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: graphlan\n owner: iuc\n revisions: 8f62f666dcb6\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: graphlan_annotate\n owner: iuc\n revisions: 5d6f8f0bef7c\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann\n owner: iuc\n revisions: 95bf7479d53c\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann_regroup_table\n owner: iuc\n revisions: 79706f10d680\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann_rename_table\n owner: iuc\n revisions: 172920f67a84\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann_renorm_table\n owner: iuc\n revisions: d7e9a3c41657\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann_split_stratified_table\n owner: iuc\n revisions: 64bc7acc22a9\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann_unpack_pathways\n owner: iuc\n revisions: '080ea153677c'\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan\n owner: iuc\n revisions: ec368db926f4\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 135b80fb1ac2\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sortmerna\n owner: rnateam\n revisions: eb35257d2e29\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metatranscriptomics/tutorial.json",
- "contributions": {
- "authorship": [
- "pratikdjagtap",
- "subinamehta",
- "jraysajulga",
- "bebatut",
- "emmaleith",
- "pravs3683",
- "shiltemann",
- "paulzierep",
- "EngyNasr"
- ],
- "reviewing": [
- "shiltemann",
- "bebatut",
- "hexylena"
- ]
- },
"contributors": [
{
"email": "pjagtap@umn.edu",
@@ -428960,94 +391570,6 @@
"orcid": "0000-0001-9047-4215",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/EngyNasr.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/microbiome/tutorials/metatranscriptomics",
@@ -429059,26 +391581,26 @@
"topic_0080"
],
"edam_operation": [
- "Visualisation",
- "Phylogenetic analysis",
- "Sequencing quality control",
- "Read pre-processing",
- "Phylogenetic inference",
- "Sequence alignment analysis",
- "Sequence similarity search",
- "Validation",
- "Species frequency estimation",
"Phylogenetic tree editing",
- "Nucleic acid sequence analysis",
- "Statistical calculation",
- "Primer removal",
- "Taxonomic classification",
- "Phylogenetic tree visualisation",
+ "Validation",
"Conversion",
+ "Sequencing quality control",
"Sequence composition calculation",
+ "Phylogenetic inference",
+ "Sequence trimming",
+ "Phylogenetic analysis",
"Phylogenetic tree analysis",
+ "Visualisation",
"Sequence comparison",
- "Sequence trimming"
+ "Statistical calculation",
+ "Phylogenetic tree visualisation",
+ "Sequence similarity search",
+ "Taxonomic classification",
+ "Species frequency estimation",
+ "Sequence alignment analysis",
+ "Primer removal",
+ "Nucleic acid sequence analysis",
+ "Read pre-processing"
],
"edam_topic": [
"Metatranscriptomics",
@@ -429119,7 +391641,7 @@
"Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
"Visualise a community structure"
],
- "pageviews": 6183616,
+ "pageviews": 6206481,
"pub_date": "2019-11-21",
"questions": [
"How to analyze metatranscriptomics data?",
@@ -429164,26 +391686,26 @@
],
"short_id": "T00388",
"short_tools": [
- "humann",
- "humann_regroup_table",
- "multiqc",
- "bg_sortmerna",
"Cut1",
"humann_unpack_pathways",
- "fastq_paired_end_interlacer",
+ "multiqc",
"Grep1",
- "metaphlan",
- "taxonomy_krona_chart",
- "export2graphlan",
- "humann_renorm_table",
"combine_metaphlan2_humann2",
- "tp_find_and_replace",
- "fastqc",
"humann_rename_table",
- "cutadapt",
- "graphlan_annotate",
+ "taxonomy_krona_chart",
"humann_split_stratified_table",
- "graphlan"
+ "bg_sortmerna",
+ "metaphlan",
+ "graphlan_annotate",
+ "cutadapt",
+ "humann_renorm_table",
+ "fastq_paired_end_interlacer",
+ "graphlan",
+ "export2graphlan",
+ "fastqc",
+ "humann_regroup_table",
+ "tp_find_and_replace",
+ "humann"
],
"slides": true,
"slides_recordings": false,
@@ -429236,6 +391758,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -429291,10 +391817,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -429341,11 +391863,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -429390,6 +391907,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -429442,10 +391963,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -429486,10 +392003,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -429532,6 +392045,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -429584,10 +392101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -429628,10 +392141,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -429674,6 +392183,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -429727,10 +392240,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -429777,10 +392286,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -429826,6 +392331,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -429880,10 +392389,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -429920,10 +392425,10 @@
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
"1.1.2",
+ "1.1.1",
"1.0.0",
- "1.1.1"
+ "1.1.0"
]
},
{
@@ -429936,18 +392441,13 @@
"state": "exact",
"version": "1.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
- "1.1.1"
+ "1.1.1",
+ "1.1.0"
]
},
{
@@ -429990,6 +392490,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430045,10 +392549,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -430098,11 +392598,6 @@
"state": "exact",
"version": "2.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -430150,6 +392645,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430205,10 +392704,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -430252,11 +392747,6 @@
"state": "exact",
"version": "1.2.0.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -430302,6 +392792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430359,10 +392853,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -430388,8 +392878,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -430413,12 +392903,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -430428,9 +392918,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -430441,11 +392931,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -430491,6 +392976,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430544,10 +393033,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -430591,11 +393076,6 @@
"state": "exact",
"version": "0.20+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -430641,6 +393121,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430694,10 +393178,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -430741,13 +393221,6 @@
"state": "exact",
"version": "1.0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -430793,6 +393266,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430848,10 +393325,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -430895,13 +393368,6 @@
"state": "exact",
"version": "1.0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -430947,6 +393413,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -430999,10 +393469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431048,20 +393514,12 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "3.6.0+galaxy0",
- "3.0.0+galaxy1"
+ "3.0.0+galaxy1",
+ "3.6.0+galaxy0"
]
},
{
@@ -431104,6 +393562,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -431156,10 +393618,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431205,14 +393663,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -431259,157 +393709,7 @@
"state": "missing"
},
{
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- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
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- {
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- "state": "missing"
- },
- {
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- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
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- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
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- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
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- {
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- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "3.6.0+galaxy0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "3.6.0+galaxy0"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "3.6.0+galaxy0"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "3.6.0+galaxy0"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "3.6.0+galaxy0"
- },
- {
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- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -431464,10 +393764,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431504,8 +393800,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
{
@@ -431513,14 +393809,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -431544,7 +393832,7 @@
"version": "3.6.0+galaxy0"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.6.0+galaxy0",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -431566,6 +393854,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -431618,10 +393910,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431658,8 +393946,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
{
@@ -431668,13 +393956,151 @@
"version": "3.6.0+galaxy0"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "3.6.0+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "3.6.0+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "3.6.0+galaxy0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "3.6.0+galaxy0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.6.0+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "3.6.0+galaxy0"
+ },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -431720,6 +394146,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -431772,10 +394202,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431821,14 +394247,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -431874,6 +394292,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -431898,8 +394320,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2"
+ "4.1.1+galaxy2",
+ "4.1.1+galaxy1"
]
},
{
@@ -431934,10 +394356,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -431985,18 +394403,6 @@
"state": "exact",
"version": "4.0.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2",
- "4.1.1+galaxy3",
- "4.0.6+galaxy3",
- "4.0.6+galaxy2",
- "4.1.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -432044,6 +394450,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -432098,10 +394508,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -432150,11 +394556,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -432165,8 +394566,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -432209,6 +394610,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -432248,8 +394653,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -432272,10 +394677,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -432318,8 +394719,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -432334,11 +394735,6 @@
"state": "exact",
"version": "4.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -432386,6 +394782,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -432440,10 +394840,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -432487,11 +394883,6 @@
"state": "exact",
"version": "2.1b.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1b.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -432564,8 +394955,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 267,
- "visitors": 2245945,
+ "visit_duration": 266,
+ "visitors": 2256698,
"workflows": [
{
"creators": [
@@ -432682,7 +395073,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nT1A_forward\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nT1A_reverse\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 1: Preprocessing\"];\n style 2 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 2: Community Profile\"];\n style 3 fill:#edd,stroke:#900,stroke-width:4px;\n 2 -->|Cutadapt on input datasets: Read 1 Output| 3;\n 2 -->|Cutadapt on input datasets: Read 2 Output| 3;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 3: Functional Information\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 2 -->|FASTQ interlacer pairs from input datasets| 4;\n 3 -->|MetaPhlAn on input datasets: Predicted taxon relative abundances| 4;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Main Metatranscriptomics Analysis",
"outputs": [],
"parent_id": "microbiome/metatranscriptomics",
@@ -433499,36 +395890,36 @@
"topic_0080"
],
"edam_operation": [
- "Phylogenetic tree generation (from molecular sequences)",
- "Multiple sequence alignment",
- "Visualisation",
- "Variant calling",
- "Data handling",
- "Sequencing quality control",
- "Sequence alignment analysis",
- "Pairwise sequence alignment",
- "De-novo assembly",
"Validation",
- "Box-Whisker plot plotting",
- "Mapping",
- "Antimicrobial resistance prediction",
+ "Phylogenetic tree generation",
+ "Sequence assembly visualisation",
+ "Cross-assembly",
+ "Sequencing quality control",
"Phylogenetic tree generation (maximum likelihood and Bayesian methods)",
+ "Data handling",
+ "Sequence composition calculation",
+ "Sequence contamination filtering",
+ "Antimicrobial resistance prediction",
+ "Mapping",
"Multilocus sequence typing",
"Sequence assembly",
- "Scatter plot plotting",
- "Statistical calculation",
- "Phylogenetic tree reconstruction",
- "Phylogenetic tree generation",
- "Genome assembly",
+ "De-novo assembly",
+ "Phylogenetic tree analysis",
+ "Visualisation",
+ "Multiple sequence alignment",
+ "Pairwise sequence alignment",
"Base-calling",
- "Mapping assembly",
+ "Genome assembly",
+ "Statistical calculation",
+ "Variant calling",
"Taxonomic classification",
+ "Sequence alignment analysis",
+ "Phylogenetic tree generation (from molecular sequences)",
"Aggregation",
- "Sequence assembly visualisation",
- "Sequence composition calculation",
- "Phylogenetic tree analysis",
- "Cross-assembly",
- "Sequence contamination filtering"
+ "Mapping assembly",
+ "Phylogenetic tree reconstruction",
+ "Scatter plot plotting",
+ "Box-Whisker plot plotting"
],
"edam_topic": [
"Metagenomics",
@@ -433564,7 +395955,7 @@
"Identify pathogens via SNP calling and build the consensus gemone of the samples",
"Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps"
],
- "pageviews": 3961,
+ "pageviews": 4035,
"pub_date": "2023-01-26",
"questions": [
"What are the preprocessing steps to prepare ONT sequencing data for further analysis?",
@@ -433606,67 +395997,67 @@
],
"short_id": "T00393",
"short_tools": [
- "tp_cut_tool",
- "tp_replace_in_column",
- "flye",
- "Add_a_column1",
- "tp_sorted_uniq",
- "minimap2",
+ "samtools_depth",
+ "__FILTER_FAILED_DATASETS__",
+ "ggplot2_heatmap",
+ "Cut1",
"fastp",
- "bcftools_norm",
"CONVERTER_gz_to_uncompressed",
- "Grouping1",
- "samtools_coverage",
- "Paste1",
"fasta_merge_files_and_filter_unique_sequences",
- "tab2fasta",
- "add_line_to_file",
- "Remove beginning1",
"multiqc",
- "snpSift_extractFields",
- "abricate",
- "compose_text_param",
- "param_value_from_file",
- "bedtools_getfastabed",
- "Cut1",
- "kraken2",
- "bandage_image",
- "collapse_dataset",
- "Grep1",
- "bcftools_consensus",
- "collection_column_join",
- "tp_multijoin_tool",
+ "split_file_to_collection",
"nanoplot",
- "tp_split_on_column",
- "regex1",
+ "Grep1",
+ "add_line_to_file",
+ "tp_head_tool",
+ "collection_element_identifiers",
"clustalw",
- "taxonomy_krona_chart",
- "krakentools_extract_kraken_reads",
- "snpSift_filter",
- "ggplot2_heatmap",
+ "porechop",
"mlst",
- "samtools_depth",
- "tp_head_tool",
- "tp_find_and_replace",
- "fasttree",
+ "taxonomy_krona_chart",
+ "snpSift_extractFields",
+ "tp_replace_in_column",
+ "minimap2",
+ "bandage_image",
+ "bamtools_split_mapped",
+ "clair3",
+ "Add_a_column1",
+ "bedtools_getfastabed",
+ "Count1",
"table_compute",
- "fastqc",
- "__FILTER_EMPTY_DATASETS__",
+ "tp_split_on_column",
"regexColumn1",
- "collection_element_identifiers",
+ "bcftools_norm",
+ "Paste1",
+ "tp_cut_tool",
+ "fasttree",
+ "samtools_fastx",
+ "collection_column_join",
+ "tp_sorted_uniq",
+ "compose_text_param",
"__BUILD_LIST__",
- "newick_display",
- "clair3",
- "split_file_to_collection",
- "medaka_consensus_pipeline",
- "fasta2tab",
- "Count1",
- "porechop",
- "bamtools_split_mapped",
+ "krakentools_extract_kraken_reads",
"barchart_gnuplot",
+ "__FILTER_EMPTY_DATASETS__",
+ "fasta2tab",
+ "fastqc",
+ "tab2fasta",
"krakentools_kreport2krona",
- "samtools_fastx",
- "__FILTER_FAILED_DATASETS__"
+ "Remove beginning1",
+ "medaka_consensus_pipeline",
+ "flye",
+ "samtools_coverage",
+ "abricate",
+ "kraken2",
+ "newick_display",
+ "snpSift_filter",
+ "collapse_dataset",
+ "Grouping1",
+ "bcftools_consensus",
+ "tp_multijoin_tool",
+ "tp_find_and_replace",
+ "regex1",
+ "param_value_from_file"
],
"slides": false,
"slides_recordings": false,
@@ -433709,6 +396100,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -433764,10 +396159,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -433814,11 +396205,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -433863,6 +396249,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -433915,10 +396305,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -433959,10 +396345,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -434005,6 +396387,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -434057,10 +396443,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434101,10 +396483,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -434147,6 +396525,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -434199,10 +396581,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434244,7 +396622,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Grep1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -434267,7 +396779,7 @@
"version": "local"
},
{
- "id": "Grep1",
+ "id": "Grouping1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -434290,145 +396802,7 @@
"state": "local"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "local"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "local"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "local"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "local"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "local"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "local"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "local"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "local"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "local"
- }
- ],
- "version": "local"
- },
- {
- "id": "Grouping1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "local"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -434483,10 +396857,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434527,10 +396897,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -434573,6 +396939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -434625,10 +396995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434669,10 +397035,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -434715,6 +397077,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -434767,10 +397133,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434811,10 +397173,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -434857,6 +397215,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -434909,10 +397271,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -434953,10 +397311,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -435000,154 +397354,16 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "local"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "local"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "local"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "local"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
- {
- "server": "https://usegalaxy.no/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "local"
- },
- {
- "id": "__FILTER_FAILED_DATASETS__",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
- },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://dintor.eurac.edu/",
@@ -435193,10 +397409,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -435238,7 +397450,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "__FILTER_FAILED_DATASETS__",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "local"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -435283,6 +397629,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -435335,10 +397685,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -435379,10 +397725,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -435425,6 +397767,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -435477,10 +397823,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -435521,10 +397863,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -435567,6 +397905,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -435619,10 +397961,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -435666,10 +398004,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -435714,6 +398048,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -435770,10 +398108,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -435820,11 +398154,6 @@
"state": "exact",
"version": "2.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -435870,6 +398199,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -435926,10 +398259,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -435976,17 +398305,12 @@
"state": "exact",
"version": "2.9.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.6",
"2.9+galaxy0",
+ "2.6",
"2.8.3+galaxy0",
"2.9.3+galaxy0",
"2.6+galaxy0"
@@ -436032,6 +398356,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436085,10 +398413,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -436131,11 +398455,6 @@
"state": "exact",
"version": "0.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -436181,6 +398500,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436213,8 +398536,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.4.0",
- "0.5.1"
+ "0.5.1",
+ "0.4.0"
]
},
{
@@ -436237,10 +398560,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -436291,11 +398610,6 @@
"state": "exact",
"version": "0.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -436341,6 +398655,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436399,10 +398717,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -436452,11 +398766,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -436504,6 +398813,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436558,10 +398871,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -436598,10 +398907,10 @@
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
"1.1.2",
+ "1.1.1",
"1.0.0",
- "1.1.1"
+ "1.1.0"
]
},
{
@@ -436614,18 +398923,13 @@
"state": "exact",
"version": "1.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
- "1.1.1"
+ "1.1.1",
+ "1.1.0"
]
},
{
@@ -436668,6 +398972,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436726,10 +399034,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -436779,11 +399083,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -436831,6 +399130,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -436889,10 +399192,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -436944,11 +399243,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -436997,6 +399291,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437055,10 +399353,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -437112,11 +399406,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -437167,6 +399456,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437225,10 +399518,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -437278,11 +399567,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -437330,6 +399614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437385,10 +399673,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -437438,11 +399722,6 @@
"state": "exact",
"version": "2.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -437490,6 +399769,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437548,10 +399831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -437598,11 +399877,6 @@
"state": "exact",
"version": "2.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -437650,6 +399924,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437710,10 +399988,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -437747,9 +400021,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -437763,11 +400037,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -437813,6 +400082,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -437866,10 +400139,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -437914,11 +400183,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -437964,6 +400228,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438021,10 +400289,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -438050,8 +400314,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -438075,12 +400339,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -438090,9 +400354,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -438103,11 +400367,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -438153,6 +400412,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438178,8 +400441,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -438216,10 +400479,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -438243,8 +400502,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -438264,12 +400523,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -438282,11 +400541,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -438335,6 +400589,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438389,10 +400647,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -438437,11 +400691,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -438487,6 +400736,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438540,10 +400793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -438588,11 +400837,6 @@
"state": "exact",
"version": "1.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -438638,6 +400882,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438694,10 +400942,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -438745,11 +400989,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -438795,6 +401034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -438851,10 +401094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -438902,11 +401141,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -438952,6 +401186,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439006,10 +401244,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -439042,11 +401276,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.9.3",
"0.8",
+ "0.9.8",
"0.9.7",
"0.1.0",
- "0.9.8"
+ "0.9.3"
]
},
{
@@ -439059,11 +401293,6 @@
"state": "exact",
"version": "1.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -439109,6 +401338,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439162,10 +401395,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -439210,10 +401439,6 @@
"state": "exact",
"version": "2.5.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -439258,6 +401483,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439282,8 +401511,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.8.1+galaxy0+galaxy0",
"0.8.1+galaxy4",
+ "0.8.1+galaxy0+galaxy0",
"2022.09+galaxy4"
]
},
@@ -439323,10 +401552,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -439376,11 +401601,6 @@
"state": "exact",
"version": "0.8.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -439426,6 +401646,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439483,10 +401707,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -439536,11 +401756,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -439586,6 +401801,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439642,10 +401861,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -439680,10 +401895,10 @@
"state": "inexact",
"versions": [
"1.9+galaxy2",
- "1.9+galaxy1",
- "1.10",
+ "1.9",
"1.4.0",
- "1.9"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -439696,18 +401911,13 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -439750,6 +401960,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439808,10 +402022,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -439861,11 +402071,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -439878,10 +402083,10 @@
"1.15.1+galaxy3",
"1.10+galaxy1",
"1.9+galaxy2",
- "1.10",
"1.4.0",
- "1.15.1+galaxy2",
- "1.15.1+galaxy4"
+ "1.10",
+ "1.15.1+galaxy4",
+ "1.15.1+galaxy2"
]
},
{
@@ -439890,12 +402095,12 @@
"versions": [
"1.15.1+galaxy3",
"1.10+galaxy1",
- "1.10",
- "1.4.0",
"1.9",
- "1.15.1+galaxy0",
+ "1.4.0",
+ "1.10",
+ "1.15.1+galaxy4",
"1.15.1+galaxy2",
- "1.15.1+galaxy4"
+ "1.15.1+galaxy0"
]
},
{
@@ -439928,6 +402133,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -439986,10 +402195,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -440035,11 +402240,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -440059,8 +402259,8 @@
"1.9",
"1.4.0.0",
"1.15.1+galaxy3",
- "1.15.1+galaxy0",
- "1.15.1+galaxy2"
+ "1.15.1+galaxy2",
+ "1.15.1+galaxy0"
]
},
{
@@ -440093,6 +402293,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440129,8 +402333,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.29.2",
- "2.30.0"
+ "2.30.0",
+ "2.29.2"
]
},
{
@@ -440153,10 +402357,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -440192,12 +402392,12 @@
"versions": [
"2.27.1",
"2.27.0.1",
- "2.29.2",
"2.30.0",
+ "2.29.2",
"2.31.1+galaxy0",
+ "2.19.0",
"2.24.0",
- "2.29.0",
- "2.19.0"
+ "2.29.0"
]
},
{
@@ -440210,17 +402410,12 @@
"state": "exact",
"version": "2.30.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.29.2",
"2.30.0",
+ "2.29.2",
"2.19.0"
]
},
@@ -440264,6 +402459,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440317,10 +402516,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -440363,10 +402558,6 @@
"state": "exact",
"version": "0.1.12+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -440413,6 +402604,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440466,10 +402661,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -440514,11 +402705,6 @@
"state": "exact",
"version": "0.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -440564,6 +402750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440618,10 +402808,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -440666,11 +402852,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -440716,6 +402897,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440768,10 +402953,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -440815,11 +402996,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -440864,6 +403040,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -440921,10 +403101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -440973,11 +403149,6 @@
"state": "exact",
"version": "0.20.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -441026,6 +403197,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441090,10 +403265,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -441129,11 +403300,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -441148,11 +403319,6 @@
"state": "exact",
"version": "0.23.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -441169,9 +403335,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -441212,6 +403378,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441266,10 +403436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -441314,11 +403480,6 @@
"state": "exact",
"version": "2.1.10+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.10+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -441364,6 +403525,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441419,10 +403584,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -441468,11 +403629,6 @@
"state": "exact",
"version": "3.4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -441521,6 +403677,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441575,10 +403735,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -441612,8 +403768,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -441626,11 +403782,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -441676,6 +403827,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441729,10 +403884,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -441775,11 +403926,6 @@
"state": "exact",
"version": "1.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -441824,6 +403970,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -441879,10 +404029,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -441925,11 +404071,6 @@
"state": "exact",
"version": "1.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -441974,6 +404115,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -442006,9 +404151,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
+ "1.0.3+galaxy1",
"1.0.3+galaxy2",
- "1.3.2+galaxy0",
- "1.0.3+galaxy1"
+ "1.3.2+galaxy0"
]
},
{
@@ -442031,10 +404176,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -442080,11 +404221,6 @@
"state": "exact",
"version": "1.7.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -442135,6 +404271,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -442169,8 +404309,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -442194,7 +404334,162 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
+ "2.27+galaxy0"
+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "2.17+galaxy0",
+ "2.17+galaxy1",
+ "2.3",
+ "2.5+gx1",
+ "2.12",
+ "2.17",
+ "2.5"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.26+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.24+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2.24+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "2.24+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2.24+galaxy0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "2.24+galaxy0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "2.28+galaxy0"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "2.28+galaxy0"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -442233,176 +404528,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
- "2.12",
- "2.5",
- "2.17+galaxy1"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2.26+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "2.24+galaxy0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.24+galaxy0"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "2.24+galaxy0"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "2.24+galaxy0"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.24+galaxy0"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "2.24+galaxy0"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
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- "state": "missing"
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- "state": "missing"
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- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
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- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "2.28+galaxy0"
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- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "2.28+galaxy0"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
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"2.5+gx1",
- "2.3",
- "2.17",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -442417,11 +404548,6 @@
"state": "exact",
"version": "2.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -442470,6 +404596,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -442523,10 +404653,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -442572,11 +404698,6 @@
"state": "exact",
"version": "2.22.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.22.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -442622,6 +404743,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -442676,10 +404801,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -442732,11 +404853,6 @@
"state": "exact",
"version": "1.11+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -442782,6 +404898,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -442836,10 +404956,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -442888,11 +405004,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -442903,8 +405014,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -442947,6 +405058,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443006,10 +405121,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -443058,11 +405169,6 @@
"state": "exact",
"version": "1.28.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -443108,6 +405214,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443169,10 +405279,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -443226,11 +405332,6 @@
"state": "exact",
"version": "1.42.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.42.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -443280,6 +405381,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443333,10 +405438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -443380,11 +405481,6 @@
"state": "exact",
"version": "1.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -443430,6 +405526,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443486,10 +405586,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -443537,10 +405633,6 @@
"state": "exact",
"version": "0.2.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -443586,6 +405678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443640,10 +405736,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -443689,10 +405781,6 @@
"state": "exact",
"version": "0.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -443738,6 +405826,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443793,10 +405885,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -443839,11 +405927,6 @@
"state": "exact",
"version": "1.15.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -443888,6 +405971,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -443923,8 +406010,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.8",
- "1.15.1+galaxy0"
+ "1.15.1+galaxy0",
+ "1.8"
]
},
{
@@ -443947,10 +406034,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -443998,11 +406081,6 @@
"state": "exact",
"version": "1.15.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -444055,6 +406133,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -444113,10 +406195,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -444165,11 +406243,6 @@
"state": "exact",
"version": "1.15.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -444219,6 +406292,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -444273,10 +406350,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -444321,11 +406394,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -444371,6 +406439,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -444427,10 +406499,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -444475,11 +406543,6 @@
"state": "exact",
"version": "4.3+t.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -444525,6 +406588,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -444579,10 +406646,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -444629,11 +406692,6 @@
"state": "exact",
"version": "1.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -444679,6 +406737,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -444733,10 +406795,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -444784,11 +406842,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -444916,7 +406969,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 180,
- "visitors": 2638,
+ "visitors": 2685,
"workflows": [
{
"creators": [
@@ -445042,7 +407095,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreference_genome_of_tested_strain\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Convert compressed file to uncompressed.\"];\n 2 -->|output| 3;\n 9d6bde4a-7180-4097-9ffd-6992111a617c[\"Output\\ndecompressed_rg_file\"];\n 3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;\n style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;\n 4[\"Map with minimap2\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n 3 -->|output1| 4;\n 31779c23-4f26-418e-9418-2551e883dbe7[\"Output\\nmap_with_minimap2\"];\n 4 --> 31779c23-4f26-418e-9418-2551e883dbe7;\n style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;\n 5[\"Clair3\"];\n 4 -->|alignment_output| 5;\n 3 -->|output1| 5;\n 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53[\"Output\\nclair3_pileup_vcf\"];\n 5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;\n style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;\n 987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"];\n 5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;\n fab82215-f59a-43b1-92d7-37629a1fdb65[\"Output\\nclair3_merged_output\"];\n 5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n 6[\"Samtools depth\"];\n 4 -->|alignment_output| 6;\n 7[\"Samtools coverage\"];\n 4 -->|alignment_output| 7;\n 8[\"bcftools norm\"];\n 5 -->|merge_output| 8;\n 3 -->|output1| 8;\n 22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\nnormalized_vcf_output\"];\n 8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n 9[\"Advanced Cut\"];\n 6 -->|output| 9;\n 10[\"Remove beginning\"];\n 7 -->|output| 10;\n 11[\"SnpSift Filter\"];\n 8 -->|output_file| 11;\n 3e7981ec-2205-4571-93eb-10c0dd14b288[\"Output\\nquality_filtered_vcf_output\"];\n 11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;\n style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;\n 12[\"Table Compute\"];\n 9 -->|output| 12;\n 13[\"Cut\"];\n 10 -->|out_file1| 13;\n 14[\"SnpSift Extract Fields\"];\n 11 -->|output| 14;\n 1b0f4f2c-4717-45be-b580-fe10cba78c35[\"Output\\nextracted_fields_from_the_vcf_output\"];\n 14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;\n style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;\n 15[\"bcftools consensus\"];\n 11 -->|output| 15;\n 3 -->|output1| 15;\n 49497f3c-9332-4924-bcfd-cb71788ad2c2[\"Output\\nbcftools_consensus\"];\n 15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;\n style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;\n 16[\"Select first\"];\n 13 -->|out_file1| 16;\n 17[\"Remove beginning\"];\n 14 -->|output| 17;\n 18[\"Collapse Collection\"];\n 16 -->|outfile| 18;\n 5ee1c158-1a85-45ca-9abd-b30632b3092c[\"Output\\nmapping_coverage_percentage_per_sample\"];\n 18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;\n style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;\n 19[\"Count\"];\n 17 -->|out_file1| 19;\n 20[\"Advanced Cut\"];\n 18 -->|output| 20;\n 21[\"Cut\"];\n 19 -->|out_file1| 21;\n 22[\"Paste\"];\n 20 -->|output| 22;\n 12 -->|table| 22;\n 25b7b87b-5ef1-487f-90cc-81351a2f81ce[\"Output\\nmapping_mean_depth_per_sample\"];\n 22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;\n style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;\n 23[\"Select first\"];\n 21 -->|out_file1| 23;\n 24[\"Collapse Collection\"];\n 23 -->|outfile| 24;\n 25[\"Column Regex Find And Replace\"];\n 24 -->|output| 25;\n 2852c4ee-24ea-4df7-b59e-54eb6e2f470b[\"Output\\nnumber_of_variants_per_sample\"];\n 25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;\n style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Allele-based Pathogen Identification",
"outputs": [
{
@@ -445806,7 +407859,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Extract element identifiers\"];\n 0 -->|output| 1;\n d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"];\n 1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n style d82a93c6-23a9-4f85-879c-ecd759a31087 stroke:#2c3143,stroke-width:4px;\n 2[\"Build list\"];\n 0 -->|output| 2;\n f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"];\n 2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d stroke:#2c3143,stroke-width:4px;\n 3[\"Split file\"];\n 1 -->|output| 3;\n eb5317bd-4bad-4cad-9219-3ac379221d6e[\"Output\\nsplitted_extracted_samples_IDs\"];\n 3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;\n style eb5317bd-4bad-4cad-9219-3ac379221d6e stroke:#2c3143,stroke-width:4px;\n 4[\"Flye\"];\n 2 -->|output| 4;\n ff0d8c7b-2ac7-4c6d-a110-f71418dad938[\"Output\\nflye_consensus_fasta\"];\n 4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;\n style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;\n 2385436f-fbe8-4d77-a40b-27a097d02941[\"Output\\nflye_assembly_graph\"];\n 4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;\n style 2385436f-fbe8-4d77-a40b-27a097d02941 stroke:#2c3143,stroke-width:4px;\n 0e42ce51-c46b-45d8-baa4-45c0e98ac712[\"Output\\nflye_assembly_gfa\"];\n 4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;\n style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;\n 3f297aed-7cee-4999-bbf4-69d84de6b64f[\"Output\\nflye_assembly_info_tabular\"];\n 4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;\n style 3f297aed-7cee-4999-bbf4-69d84de6b64f stroke:#2c3143,stroke-width:4px;\n 5[\"Parse parameter value\"];\n 3 -->|list_output_txt| 5;\n 3608e170-c462-42a2-8003-f3f65baa3834[\"Output\\nparsed_extracted_samples_IDs_to_text\"];\n 5 --> 3608e170-c462-42a2-8003-f3f65baa3834;\n style 3608e170-c462-42a2-8003-f3f65baa3834 stroke:#2c3143,stroke-width:4px;\n 6[\"medaka consensus pipeline\"];\n 4 -->|consensus| 6;\n 0 -->|output| 6;\n 9e5ad6ec-b408-4132-ba07-dec9fa626923[\"Output\\nmedaka_gaps_in_draft_bed_file\"];\n 6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;\n style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;\n fcbd3e3f-2e93-4798-b696-dad7db9f2efd[\"Output\\nmedaka_log_file\"];\n 6 --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;\n style fcbd3e3f-2e93-4798-b696-dad7db9f2efd stroke:#2c3143,stroke-width:4px;\n 60656aac-ad2a-4c9b-9a68-b9fb18ae5595[\"Output\\nmedaka_propability_h5_file\"];\n 6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;\n style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;\n c790d434-8e78-4df0-a0d4-8f9da0692158[\"Output\\nmedaka_calls_of_draft_bam_file\"];\n 6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;\n style c790d434-8e78-4df0-a0d4-8f9da0692158 stroke:#2c3143,stroke-width:4px;\n df361e19-b6d1-405b-96cc-b48c1ab7c604[\"Output\\nsample_all_contigs\"];\n 6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;\n style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;\n 7[\"Bandage Image\"];\n 4 -->|assembly_gfa| 7;\n 9612a851-1f94-4d54-b001-5d082bcc9055[\"Output\\nbandage_assembly_graph_image\"];\n 7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;\n style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;\n 8[\"Compose text parameter value\"];\n 5 -->|text_param| 8;\n 9[\"FASTA-to-Tabular\"];\n 6 -->|out_consensus| 9;\n de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\nsample_specific_contigs_tabular_file_preparation\"];\n 9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n 10[\"ABRicate\"];\n 6 -->|out_consensus| 10;\n 8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n 10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n 11[\"ABRicate\"];\n 6 -->|out_consensus| 11;\n fa021d98-d885-4834-ac62-f30d5792260e[\"Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n 11 --> fa021d98-d885-4834-ac62-f30d5792260e;\n style fa021d98-d885-4834-ac62-f30d5792260e stroke:#2c3143,stroke-width:4px;\n 12[\"Replace\"];\n 8 -->|out1| 12;\n 9 -->|output| 12;\n 174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"];\n 12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;\n style 174cb2c3-ed28-453c-8afb-85150e0b51ad stroke:#2c3143,stroke-width:4px;\n 13[\"Replace\"];\n 8 -->|out1| 13;\n 10 -->|report| 13;\n 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad[\"Output\\nvfs\"];\n 13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;\n style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad stroke:#2c3143,stroke-width:4px;\n 14[\"Replace\"];\n 8 -->|out1| 14;\n 11 -->|report| 14;\n a8eb74a5-362b-4f0f-a944-672e27981a41[\"Output\\namrs\"];\n 14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;\n style a8eb74a5-362b-4f0f-a944-672e27981a41 stroke:#2c3143,stroke-width:4px;\n 15[\"Tabular-to-FASTA\"];\n 12 -->|outfile| 15;\n a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe[\"Output\\ncontigs\"];\n 15 --> a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;\n style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Gene-based Pathogen Identification",
"outputs": [
{
@@ -446876,7 +408929,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\ncollection_of_all_samples\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Porechop\"];\n 1 -->|output| 2;\n 34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"Output\\nporechop_output_trimmed_reads\"];\n 2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n 3[\"NanoPlot\"];\n 1 -->|output| 3;\n 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n 3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n 304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n 3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n style 304110f9-60d0-4ba2-8b3b-fae0e2a49554 stroke:#2c3143,stroke-width:4px;\n f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n 3 --> f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC\"];\n 1 -->|output| 4;\n d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"];\n 4 --> d0a64624-05d0-4068-835b-a025fc011760;\n style d0a64624-05d0-4068-835b-a025fc011760 stroke:#2c3143,stroke-width:4px;\n e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n 4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n 5[\"fastp\"];\n 2 -->|outfile| 5;\n a2219483-50b7-4aed-98dd-333ad2e12eb8[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"];\n 5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n style a2219483-50b7-4aed-98dd-333ad2e12eb8 stroke:#2c3143,stroke-width:4px;\n 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"];\n 5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4 stroke:#2c3143,stroke-width:4px;\n 6[\"MultiQC\"];\n 4 -->|text_file| 6;\n ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"];\n 6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n style ebffe782-a56c-431f-8af4-c0cb8d7a02fc stroke:#2c3143,stroke-width:4px;\n 0f92196d-047d-4918-819d-c0ff7cd3ae85[\"Output\\nmultiQC_html_report_before_preprocessing\"];\n 6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n 7[\"Map with minimap2\"];\n 0 -->|output| 7;\n 5 -->|out1| 7;\n 9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"Output\\nbam_map_to_host\"];\n 7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n 8[\"NanoPlot\"];\n 5 -->|out1| 8;\n b5899290-4c57-4662-ad22-860654652ade[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n 8 --> b5899290-4c57-4662-ad22-860654652ade;\n style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"];\n 8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf stroke:#2c3143,stroke-width:4px;\n 42db7f93-919e-4bbb-81a1-06411a9da410[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n 8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 5 -->|out1| 9;\n 09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"];\n 9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n style 09306471-afa0-4106-9cc7-259b93dfc862 stroke:#2c3143,stroke-width:4px;\n 084f982f-20f1-457e-8012-91ebbb85633d[\"Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n 9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n 10[\"Split BAM by reads mapping status\"];\n 7 -->|alignment_output| 10;\n 14a53fe2-f296-43aa-86b7-243278c1050c[\"Output\\nnon_host_sequences_bam\"];\n 10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;\n style 14a53fe2-f296-43aa-86b7-243278c1050c stroke:#2c3143,stroke-width:4px;\n 3b1e626f-6bc1-484c-be01-366534361b73[\"Output\\nhost_sequences_bam\"];\n 10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;\n 11[\"Select\"];\n 9 -->|text_file| 11;\n a809853b-119f-44d2-986b-8d2006439fbe[\"Output\\ntotal_sequences_before_hosts_sequences_removal\"];\n 11 --> a809853b-119f-44d2-986b-8d2006439fbe;\n style a809853b-119f-44d2-986b-8d2006439fbe stroke:#2c3143,stroke-width:4px;\n 12[\"Samtools fastx\"];\n 10 -->|mapped| 12;\n 10d4eaec-81d8-444e-8075-7b77a1fb6870[\"Output\\nhost_sequences_fastq\"];\n 12 --> 10d4eaec-81d8-444e-8075-7b77a1fb6870;\n style 10d4eaec-81d8-444e-8075-7b77a1fb6870 stroke:#2c3143,stroke-width:4px;\n 13[\"Samtools fastx\"];\n 10 -->|unmapped| 13;\n 0c2dd74d-ac4f-45cf-839c-50386a7ece28[\"Output\\nnon_host_sequences_fastq\"];\n 13 --> 0c2dd74d-ac4f-45cf-839c-50386a7ece28;\n style 0c2dd74d-ac4f-45cf-839c-50386a7ece28 stroke:#2c3143,stroke-width:4px;\n 14[\"Collapse Collection\"];\n 11 -->|out_file1| 14;\n 15[\"Filter failed datasets\"];\n 12 -->|output| 15;\n 16[\"Kraken2\"];\n 13 -->|output| 16;\n 203d303e-8f3a-4242-971f-b345842ebdb8[\"Output\\nkraken2_with_kalamri_database_output\"];\n 16 --> 203d303e-8f3a-4242-971f-b345842ebdb8;\n style 203d303e-8f3a-4242-971f-b345842ebdb8 stroke:#2c3143,stroke-width:4px;\n 843afd4d-23a8-46e7-b945-8b67dd7ae341[\"Output\\nkraken2_with_kalamri_database_report\"];\n 16 --> 843afd4d-23a8-46e7-b945-8b67dd7ae341;\n style 843afd4d-23a8-46e7-b945-8b67dd7ae341 stroke:#2c3143,stroke-width:4px;\n 17[\"Cut\"];\n 14 -->|output| 17;\n d07be9f1-d250-4008-91ee-59a68521eb56[\"Output\\nquality_retained_all_reads\"];\n 17 --> d07be9f1-d250-4008-91ee-59a68521eb56;\n style d07be9f1-d250-4008-91ee-59a68521eb56 stroke:#2c3143,stroke-width:4px;\n 18[\"FastQC\"];\n 15 -->|output| 18;\n b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7[\"Output\\nhosts_qc_text_file\"];\n 18 --> b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7;\n style b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 stroke:#2c3143,stroke-width:4px;\n b72ff57b-0921-43bf-a817-6cd444c8f3cb[\"Output\\nhosts_qc_html\"];\n 18 --> b72ff57b-0921-43bf-a817-6cd444c8f3cb;\n style b72ff57b-0921-43bf-a817-6cd444c8f3cb stroke:#2c3143,stroke-width:4px;\n 19[\"Krakentools: Extract Kraken Reads By ID\"];\n 5 -->|out1| 19;\n 16 -->|report_output| 19;\n 16 -->|output| 19;\n 57e3b725-8e13-40b2-9acc-31fd56ebc80a[\"Output\\ncollection_of_preprocessed_samples\"];\n 19 --> 57e3b725-8e13-40b2-9acc-31fd56ebc80a;\n style 57e3b725-8e13-40b2-9acc-31fd56ebc80a stroke:#2c3143,stroke-width:4px;\n 20[\"Select\"];\n 18 -->|text_file| 20;\n 3ba35c71-32f0-4741-98d4-ea8522e27500[\"Output\\ntotal_sequences_after_hosts_sequences_removal\"];\n 20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500;\n style 3ba35c71-32f0-4741-98d4-ea8522e27500 stroke:#2c3143,stroke-width:4px;\n 21[\"Collapse Collection\"];\n 20 -->|out_file1| 21;\n 22[\"Cut\"];\n 21 -->|output| 22;\n cef36c68-4549-4fd6-b7c8-71fb21df012f[\"Output\\nquality_retained_hosts_reads\"];\n 22 --> cef36c68-4549-4fd6-b7c8-71fb21df012f;\n style cef36c68-4549-4fd6-b7c8-71fb21df012f stroke:#2c3143,stroke-width:4px;\n 23[\"Column join\"];\n 17 -->|out_file1| 23;\n 22 -->|out_file1| 23;\n 24[\"Compute\"];\n 23 -->|tabular_output| 24;\n 25[\"Column Regex Find And Replace\"];\n 24 -->|out_file1| 25;\n 470892ee-dab9-48d7-ad97-45dbd52afaa7[\"Output\\nremoved_hosts_percentage_tabular\"];\n 25 --> 470892ee-dab9-48d7-ad97-45dbd52afaa7;\n style 470892ee-dab9-48d7-ad97-45dbd52afaa7 stroke:#2c3143,stroke-width:4px;\n 26[\"MultiQC\"];\n 9 -->|text_file| 26;\n 25 -->|out_file1| 26;\n 0b1b5a73-36ee-42a2-a220-1ced6ec7378b[\"Output\\nmultiQC_html_report_after_preprocessing\"];\n 26 --> 0b1b5a73-36ee-42a2-a220-1ced6ec7378b;\n style 0b1b5a73-36ee-42a2-a220-1ced6ec7378b stroke:#2c3143,stroke-width:4px;\n 13cbf6c7-6954-4458-aa66-a5b020c63822[\"Output\\nmultiQC_stats_after_preprocessing\"];\n 26 --> 13cbf6c7-6954-4458-aa66-a5b020c63822;\n style 13cbf6c7-6954-4458-aa66-a5b020c63822 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Nanopore Preprocessing",
"outputs": [
{
@@ -448647,7 +410700,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\namr_identified_by_ncbi\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nvfs_of_genes_identified_by_vfdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nremoved_hosts_percentage_tabular\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nmapping_mean_depth_per_sample\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Collection\\namrs\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nmapping_coverage_percentage_per_sample\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nnumber_of_variants_per_sample\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Collection\\ncontigs\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"\u2139\ufe0f Input Collection\\nvfs\"];\n style 9 stroke:#2c3143,stroke-width:4px;\n 10[\"Filter failed datasets\"];\n 0 -->|output| 10;\n 11[\"Filter failed datasets\"];\n 1 -->|output| 11;\n 12[\"Bar chart\"];\n 3 -->|output| 12;\n 0961166e-38b6-44e3-93db-100d821b0070[\"Output\\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"];\n 12 --> 0961166e-38b6-44e3-93db-100d821b0070;\n style 0961166e-38b6-44e3-93db-100d821b0070 stroke:#2c3143,stroke-width:4px;\n 13[\"Bar chart\"];\n 3 -->|output| 13;\n 548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"];\n 13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n style 548975e5-4619-49fc-9e95-4d7f4d761dfd stroke:#2c3143,stroke-width:4px;\n 14[\"Bar chart\"];\n 4 -->|output| 14;\n a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"];\n 14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n style a71ebb67-1154-4f25-a62d-e8fa2b839e2e stroke:#2c3143,stroke-width:4px;\n 15[\"Filter failed datasets\"];\n 5 -->|output| 15;\n 16[\"Bar chart\"];\n 6 -->|output| 16;\n 2567360e-d39f-4316-84f5-77aaf8e8198c[\"Output\\nmapping_coverage_percentage_per_sample_fig\"];\n 16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n 17[\"Bar chart\"];\n 7 -->|output| 17;\n 68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n 17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n 18[\"Filter failed datasets\"];\n 8 -->|output| 18;\n 19[\"Filter failed datasets\"];\n 9 -->|output| 19;\n 20[\"Remove beginning\"];\n 10 -->|output| 20;\n 21[\"Remove beginning\"];\n 11 -->|output| 21;\n 22[\"Remove beginning\"];\n 15 -->|output| 22;\n 23[\"Collapse Collection\"];\n 18 -->|output| 23;\n 86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"];\n 23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n style 86910e39-57bf-4a76-ac4c-739340fd2387 stroke:#2c3143,stroke-width:4px;\n 24[\"Collapse Collection\"];\n 19 -->|output| 24;\n 02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"];\n 24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n style 02b996c6-a912-4e4e-b3ec-49601faaa452 stroke:#2c3143,stroke-width:4px;\n 25[\"Remove beginning\"];\n 19 -->|output| 25;\n 26[\"Count\"];\n 20 -->|out_file1| 26;\n 27[\"Count\"];\n 21 -->|out_file1| 27;\n 28[\"Group\"];\n 21 -->|out_file1| 28;\n 29[\"Unique\"];\n 22 -->|out_file1| 29;\n 30[\"Split by group\"];\n 24 -->|output| 30;\n 59f8cb09-424b-47b1-b94b-a612c2610cab[\"Output\\nsplit_by_group_collection\"];\n 30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n 31[\"Unique\"];\n 25 -->|out_file1| 31;\n 32[\"Cut\"];\n 26 -->|out_file1| 32;\n 33[\"Cut\"];\n 27 -->|out_file1| 33;\n 34[\"Filter empty datasets\"];\n 28 -->|out_file1| 34;\n 35[\"Cut\"];\n 29 -->|outfile| 35;\n 36[\"Cut\"];\n 30 -->|split_output| 36;\n eeb25a51-ea21-4a19-a196-55d5bd919b10[\"Output\\nadjusted_abricate_vfs_tabular_part1\"];\n 36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n 37[\"Cut\"];\n 31 -->|outfile| 37;\n 38[\"Collapse Collection\"];\n 32 -->|out_file1| 38;\n 39[\"Collapse Collection\"];\n 33 -->|out_file1| 39;\n 40[\"Column join\"];\n 34 -->|output| 40;\n 41[\"bedtools getfasta\"];\n 23 -->|output| 41;\n 35 -->|out_file1| 41;\n 42[\"Remove beginning\"];\n 36 -->|out_file1| 42;\n aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\nadjusted_abricate_vfs_tabular_part2\"];\n 42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n 43[\"bedtools getfasta\"];\n 23 -->|output| 43;\n 37 -->|out_file1| 43;\n 44[\"Column Regex Find And Replace\"];\n 38 -->|output| 44;\n 4809c36b-31ef-4664-8e4e-47f0f72152de[\"Output\\namrs_count\"];\n 44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n style 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n 45[\"Column Regex Find And Replace\"];\n 39 -->|output| 45;\n 87efc81d-4d84-4af3-831f-dfe033c59f78[\"Output\\nvfs_count\"];\n 45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n style 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n 46[\"Column Regex Find And Replace\"];\n 40 -->|tabular_output| 46;\n f5c221e3-00ef-4834-9a5f-a94c97fd6764[\"Output\\nheatmap_table\"];\n 46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764;\n style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px;\n 47[\"Regex Find And Replace\"];\n 41 -->|output| 47;\n 48[\"bedtools getfasta\"];\n 23 -->|output| 48;\n 42 -->|out_file1| 48;\n 82ce2107-89a3-438c-95bb-dc871b5258b7[\"Output\\nfiltered_sequences_with_vfs_fasta\"];\n 48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;\n style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;\n 49[\"Regex Find And Replace\"];\n 43 -->|output| 49;\n 50[\"Multi-Join\"];\n 45 -->|out_file1| 50;\n 44 -->|out_file1| 50;\n 51[\"Heatmap w ggplot\"];\n 46 -->|out_file1| 51;\n c0417c91-a513-4c6a-9a62-3aac2f1f8e85[\"Output\\nheatmap_pdf\"];\n 51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85;\n style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;\n 97816bc2-fd0c-4077-a721-8dd1470879d1[\"Output\\nheatmap_png\"];\n 51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;\n style 97816bc2-fd0c-4077-a721-8dd1470879d1 stroke:#2c3143,stroke-width:4px;\n 52[\"Filter empty datasets\"];\n 47 -->|out_file1| 52;\n 53[\"ClustalW\"];\n 48 -->|output| 53;\n 9b7bd78c-f112-480b-a7df-c10711af254c[\"Output\\nclustalw_on_input_dnd\"];\n 53 --> 9b7bd78c-f112-480b-a7df-c10711af254c;\n style 9b7bd78c-f112-480b-a7df-c10711af254c stroke:#2c3143,stroke-width:4px;\n 6af20322-24da-4036-80de-37bed2d25848[\"Output\\nclustalw_on_input_clustal\"];\n 53 --> 6af20322-24da-4036-80de-37bed2d25848;\n style 6af20322-24da-4036-80de-37bed2d25848 stroke:#2c3143,stroke-width:4px;\n 54[\"Filter empty datasets\"];\n 49 -->|out_file1| 54;\n 55[\"Replace Text\"];\n 50 -->|outfile| 55;\n 91745da0-0b8d-4a7a-b927-b36107f17ec5[\"Output\\nvfs_amrs_count_table\"];\n 55 --> 91745da0-0b8d-4a7a-b927-b36107f17ec5;\n style 91745da0-0b8d-4a7a-b927-b36107f17ec5 stroke:#2c3143,stroke-width:4px;\n 56[\"FASTA-to-Tabular\"];\n 52 -->|output| 56;\n 57[\"Filter empty datasets\"];\n 53 -->|output| 57;\n 32d00c1d-68c4-4069-8d5d-023aabdfadbe[\"Output\\nfiltered_empty_datasets\"];\n 57 --> 32d00c1d-68c4-4069-8d5d-023aabdfadbe;\n style 32d00c1d-68c4-4069-8d5d-023aabdfadbe stroke:#2c3143,stroke-width:4px;\n 58[\"FASTA-to-Tabular\"];\n 54 -->|output| 58;\n 59[\"Cut\"];\n 56 -->|output| 59;\n 60[\"FASTTREE\"];\n 57 -->|output| 60;\n aacdfe45-eb0c-4f6e-a479-eeb170774757[\"Output\\nfasttree_nhx\"];\n 60 --> aacdfe45-eb0c-4f6e-a479-eeb170774757;\n style aacdfe45-eb0c-4f6e-a479-eeb170774757 stroke:#2c3143,stroke-width:4px;\n 61[\"Cut\"];\n 58 -->|output| 61;\n 62[\"Group\"];\n 59 -->|out_file1| 62;\n 63[\"Newick Display\"];\n 60 -->|output| 63;\n 0c22178c-dc85-4137-80e2-f3040b92bd20[\"Output\\nnewick_genes_tree_graphs_collection\"];\n 63 --> 0c22178c-dc85-4137-80e2-f3040b92bd20;\n style 0c22178c-dc85-4137-80e2-f3040b92bd20 stroke:#2c3143,stroke-width:4px;\n 64[\"Group\"];\n 61 -->|out_file1| 64;\n 65[\"Tabular-to-FASTA\"];\n 62 -->|out_file1| 65;\n 66[\"Tabular-to-FASTA\"];\n 64 -->|out_file1| 66;\n 67[\"FASTA Merge Files and Filter Unique Sequences\"];\n 65 -->|output| 67;\n 68[\"FASTA Merge Files and Filter Unique Sequences\"];\n 66 -->|output| 68;\n 69[\"ClustalW\"];\n 67 -->|output| 69;\n 70[\"ClustalW\"];\n 68 -->|output| 70;\n 71[\"FASTTREE\"];\n 69 -->|output| 71;\n 72[\"FASTTREE\"];\n 70 -->|output| 72;\n 73[\"Newick Display\"];\n 71 -->|output| 73;\n 1f9cb2cf-219f-48de-8058-d6d45f3b3158[\"Output\\nall_samples_phylogenetic_tree_based_amrs\"];\n 73 --> 1f9cb2cf-219f-48de-8058-d6d45f3b3158;\n style 1f9cb2cf-219f-48de-8058-d6d45f3b3158 stroke:#2c3143,stroke-width:4px;\n 74[\"Newick Display\"];\n 72 -->|output| 74;\n 6bb4b32b-7cca-4e04-8120-be9f64ccba39[\"Output\\nall_samples_phylogenetic_tree_based_vfs\"];\n 74 --> 6bb4b32b-7cca-4e04-8120-be9f64ccba39;\n style 6bb4b32b-7cca-4e04-8120-be9f64ccba39 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
"outputs": [
{
@@ -450050,7 +412103,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nkraken_database\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"Kraken2\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 26f9041f-d8a4-4f64-8a53-404d5c7e2f61[\"Output\\nkraken2_with_pluspf_database_output\"];\n 2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;\n style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;\n f2ddd05b-66a0-4cea-9da6-ed107eecbe1b[\"Output\\nkraken2_with_pluspf_database_output_report\"];\n 2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;\n style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;\n 3[\"Krakentools: Convert kraken report file\"];\n 2 -->|report_output| 3;\n c490ab8d-1b1d-4914-aa51-a62a967a4018[\"Output\\nconverted_kraken_report\"];\n 3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;\n style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;\n 4[\"Krona pie chart\"];\n 3 -->|output| 4;\n dcc857c6-f579-4c74-84ec-bb6ce3794a56[\"Output\\nkrona_pie_chart\"];\n 4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;\n style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Taxonomy Profiling and Visualization with Krona",
"outputs": [
{
@@ -450451,24 +412504,6 @@
},
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- "elixir-europe"
- ],
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- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
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}
],
"dir": "topics/microbiome/tutorials/metatranscriptomics-short",
@@ -450700,26 +412647,26 @@
"topic_0080"
],
"edam_operation": [
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- "Phylogenetic analysis",
- "Sequencing quality control",
- "Read pre-processing",
- "Phylogenetic inference",
- "Sequence alignment analysis",
- "Sequence similarity search",
- "Validation",
- "Species frequency estimation",
"Phylogenetic tree editing",
- "Nucleic acid sequence analysis",
- "Statistical calculation",
- "Primer removal",
- "Taxonomic classification",
- "Phylogenetic tree visualisation",
+ "Validation",
"Conversion",
+ "Sequencing quality control",
"Sequence composition calculation",
+ "Phylogenetic inference",
+ "Sequence trimming",
+ "Phylogenetic analysis",
"Phylogenetic tree analysis",
+ "Visualisation",
"Sequence comparison",
- "Sequence trimming"
+ "Statistical calculation",
+ "Phylogenetic tree visualisation",
+ "Sequence similarity search",
+ "Taxonomic classification",
+ "Species frequency estimation",
+ "Sequence alignment analysis",
+ "Primer removal",
+ "Nucleic acid sequence analysis",
+ "Read pre-processing"
],
"edam_topic": [
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@@ -450760,7 +412707,7 @@
"Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
"Visualise a community structure"
],
- "pageviews": 456,
+ "pageviews": 464,
"pub_date": "2020-02-13",
"questions": [
"How to analyze metatranscriptomics data?\"",
@@ -450805,26 +412752,26 @@
],
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- "humann_regroup_table",
- "multiqc",
- "bg_sortmerna",
"Cut1",
"humann_unpack_pathways",
- "fastq_paired_end_interlacer",
+ "multiqc",
"Grep1",
- "metaphlan",
- "taxonomy_krona_chart",
- "export2graphlan",
- "humann_renorm_table",
"combine_metaphlan2_humann2",
- "tp_find_and_replace",
- "fastqc",
"humann_rename_table",
- "cutadapt",
- "graphlan_annotate",
+ "taxonomy_krona_chart",
"humann_split_stratified_table",
- "graphlan"
+ "bg_sortmerna",
+ "metaphlan",
+ "graphlan_annotate",
+ "cutadapt",
+ "humann_renorm_table",
+ "fastq_paired_end_interlacer",
+ "graphlan",
+ "export2graphlan",
+ "fastqc",
+ "humann_regroup_table",
+ "tp_find_and_replace",
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],
"slides": false,
"slides_recordings": false,
@@ -450877,6 +412824,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"name": "InteractoMIX",
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},
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"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
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"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
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"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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"server": "https://usegalaxy.eu",
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"state": "local"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"state": "exact",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -452029,8 +413944,8 @@
"versions": [
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"0.72+galaxy1",
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@@ -452069,9 +413984,9 @@
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@@ -452132,6 +414042,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
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@@ -452282,6 +414187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
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{
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"state": "exact",
@@ -452434,6 +414332,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
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@@ -452489,10 +414391,6 @@
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@@ -452588,6 +414479,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
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},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -452689,20 +414580,12 @@
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{
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"state": "inexact",
"versions": [
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- "3.0.0+galaxy1"
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]
},
{
@@ -452745,6 +414628,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -452899,6 +414774,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -452951,10 +414830,6 @@
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -452997,14 +414872,6 @@
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},
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- "versions": [
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- "3.9+galaxy0"
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- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -453053,6 +414920,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453105,10 +414976,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453145,8 +415012,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
{
@@ -453154,14 +415021,6 @@
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -453207,6 +415066,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453259,10 +415122,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453305,14 +415164,6 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -453360,6 +415211,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453412,10 +415267,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453452,8 +415303,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
{
@@ -453461,14 +415312,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -453514,6 +415357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453566,10 +415413,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453612,14 +415455,6 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -453667,6 +415502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453719,10 +415558,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453759,8 +415594,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.8+galaxy0",
- "3.7+galaxy0"
+ "3.7+galaxy0",
+ "3.8+galaxy0"
]
},
{
@@ -453768,14 +415603,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -453821,6 +415648,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -453873,10 +415704,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -453919,14 +415746,6 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -453974,6 +415793,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454026,10 +415849,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -454075,14 +415894,6 @@
"state": "exact",
"version": "3.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -454128,6 +415939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454180,10 +415995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -454226,14 +416037,6 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.8+galaxy0",
- "3.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -454281,6 +416084,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454305,8 +416112,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2"
+ "4.1.1+galaxy2",
+ "4.1.1+galaxy1"
]
},
{
@@ -454341,10 +416148,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -454392,18 +416195,6 @@
"state": "exact",
"version": "4.0.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2",
- "4.1.1+galaxy3",
- "4.0.6+galaxy3",
- "4.0.6+galaxy2",
- "4.1.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -454451,6 +416242,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454505,10 +416300,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -454557,11 +416348,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -454572,8 +416358,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -454616,6 +416402,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454655,8 +416445,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -454679,10 +416469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -454725,8 +416511,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -454741,11 +416527,6 @@
"state": "exact",
"version": "4.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -454793,6 +416574,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -454847,10 +416632,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -454894,11 +416675,6 @@
"state": "exact",
"version": "2.1b.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1b.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -454976,8 +416752,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 92,
- "visitors": 358,
+ "visit_duration": 91,
+ "visitors": 362,
"workflows": [
{
"creators": [
@@ -455094,7 +416870,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nT1A_forward\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nT1A_reverse\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Quality control Forward\"];\n 0 -->|output| 2;\n 025f2766-0802-461e-afbd-a716e6f81ba8[\"Output\\nFastQC on input dataset(s): RawData\"];\n 2 --> 025f2766-0802-461e-afbd-a716e6f81ba8;\n style 025f2766-0802-461e-afbd-a716e6f81ba8 stroke:#2c3143,stroke-width:4px;\n a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd[\"Output\\nFastQC on input dataset(s): Webpage\"];\n 2 --> a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd;\n style a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd stroke:#2c3143,stroke-width:4px;\n 3[\"Quality control Reverse\"];\n 1 -->|output| 3;\n 4[\"Cutadapt\"];\n 0 -->|output| 4;\n 1 -->|output| 4;\n 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67[\"Output\\nCutadapt on input dataset(s): Read 1 Output\"];\n 4 --> 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67;\n style 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67 stroke:#2c3143,stroke-width:4px;\n 36ec0bba-e49a-47e2-b916-afec9b35cc3e[\"Output\\nCutadapt on input dataset(s): Read 2 Output\"];\n 4 --> 36ec0bba-e49a-47e2-b916-afec9b35cc3e;\n style 36ec0bba-e49a-47e2-b916-afec9b35cc3e stroke:#2c3143,stroke-width:4px;\n 5[\"MultiQC\"];\n 2 -->|text_file| 5;\n 3 -->|text_file| 5;\n b9ca2123-0ee0-40a0-b2ec-cfc94fa35849[\"Output\\nMultiQC on input dataset(s): Stats\"];\n 5 --> b9ca2123-0ee0-40a0-b2ec-cfc94fa35849;\n style b9ca2123-0ee0-40a0-b2ec-cfc94fa35849 stroke:#2c3143,stroke-width:4px;\n e94ceb7a-0d6b-41c8-b79d-035b315e0a06[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n 5 --> e94ceb7a-0d6b-41c8-b79d-035b315e0a06;\n style e94ceb7a-0d6b-41c8-b79d-035b315e0a06 stroke:#2c3143,stroke-width:4px;\n 6[\"rRNA/rDNA selection\"];\n 4 -->|out1| 6;\n 4 -->|out2| 6;\n 7[\"FASTQ interlacer\"];\n 6 -->|unaligned_forward| 7;\n 6 -->|unaligned_reverse| 7;\n b060eebc-cd14-486e-806e-aae983bdf52d[\"Output\\nFASTQ interlacer singles from input dataset(s)\"];\n 7 --> b060eebc-cd14-486e-806e-aae983bdf52d;\n style b060eebc-cd14-486e-806e-aae983bdf52d stroke:#2c3143,stroke-width:4px;\n 70b738db-5451-4eaa-91c0-eb445be297fb[\"Output\\nFASTQ interlacer pairs from input dataset(s)\"];\n 7 --> 70b738db-5451-4eaa-91c0-eb445be297fb;\n style 70b738db-5451-4eaa-91c0-eb445be297fb stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 1: Preprocessing",
"outputs": [
{
@@ -455658,7 +417434,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQC controlled forward reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nQC controlled reverse reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Taxonomic assignation\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n b3e3198d-394e-4aeb-ba6c-9e73bfe8d049[\"Output\\nMetaPhlAn on input dataset(s): SAM file\"];\n 2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049;\n style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px;\n a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b[\"Output\\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances\"];\n 2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b;\n style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px;\n 30a9e692-8d31-45bd-9246-81ddead3ba03[\"Output\\nMetaPhlAn on input dataset(s): Bowtie2 output\"];\n 2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03;\n style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px;\n 2465a9ab-a28e-4c58-b647-b6792f77ddf2[\"Output\\nMetaPhlAn on input dataset(s): BIOM file\"];\n 2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2;\n style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px;\n 3[\"Cut\"];\n 2 -->|output_file| 3;\n 4[\"Krona pie chart\"];\n 2 -->|krona_output_file| 4;\n 5[\"Export to GraPhlAn\"];\n 3 -->|out_file1| 5;\n f578de2e-6edd-4ee0-9bc4-9371d6fd957f[\"Output\\nExport to GraPhlAn on input dataset(s): Annotation\"];\n 5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f;\n style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px;\n 4e9cfae0-ee7b-4347-84db-5a3e24688e50[\"Output\\nExport to GraPhlAn on input dataset(s): Tree\"];\n 5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50;\n style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px;\n 6[\"Generation, personalization and annotation of tree\"];\n 5 -->|annotation| 6;\n 5 -->|tree| 6;\n edf4ecaf-dddd-43a3-ba4a-d683671c1815[\"Output\\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML\"];\n 6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815;\n style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px;\n 7[\"Visualisation GraPhlAn\"];\n 6 -->|output_tree| 7;\n b304fe87-de7e-48d2-8774-9c52d2395fa4[\"Output\\nGraPhlAn on input dataset(s): PNG\"];\n 7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4;\n style b304fe87-de7e-48d2-8774-9c52d2395fa4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 2: Community Profile",
"outputs": [
{
@@ -456141,7 +417917,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInterlaced non-rRNA reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Cut\"];\n 1 -->|output| 2;\n 3[\"Metabolic assignation\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 65797303-6f12-4ae8-9511-1af40f52e71d[\"Output\\nHUMAnN on input dataset(s): Pathways and their abundance\"];\n 3 --> 65797303-6f12-4ae8-9511-1af40f52e71d;\n style 65797303-6f12-4ae8-9511-1af40f52e71d stroke:#2c3143,stroke-width:4px;\n 5cae6935-448b-4af9-ad78-7b17490e4d4a[\"Output\\nHUMAnN on input dataset(s): Pathways and their coverage\"];\n 3 --> 5cae6935-448b-4af9-ad78-7b17490e4d4a;\n style 5cae6935-448b-4af9-ad78-7b17490e4d4a stroke:#2c3143,stroke-width:4px;\n 60492d72-7b3c-45c9-b32b-b6374ab08228[\"Output\\nHUMAnN on input dataset(s): Log\"];\n 3 --> 60492d72-7b3c-45c9-b32b-b6374ab08228;\n style 60492d72-7b3c-45c9-b32b-b6374ab08228 stroke:#2c3143,stroke-width:4px;\n ba124b0f-cbd5-4b65-b87a-84cfa578a927[\"Output\\nHUMAnN on input dataset(s): Gene families and their abundance\"];\n 3 --> ba124b0f-cbd5-4b65-b87a-84cfa578a927;\n style ba124b0f-cbd5-4b65-b87a-84cfa578a927 stroke:#2c3143,stroke-width:4px;\n 4[\"Renormalize\"];\n 3 -->|gene_families_tsv| 4;\n 5[\"Renormalize\"];\n 3 -->|pathabundance_tsv| 5;\n 6[\"Regroup\"];\n 3 -->|gene_families_tsv| 6;\n 7[\"Replace\"];\n 4 -->|output| 7;\n 8[\"Unpack pathway abundances\"];\n 4 -->|output| 8;\n 5 -->|output| 8;\n 9[\"Rename features\"];\n 6 -->|output| 9;\n 10[\"Split a HUMAnN table\"];\n 6 -->|output| 10;\n 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n 10 --> 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c;\n style 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c stroke:#2c3143,stroke-width:4px;\n 6a65ee93-3a2e-4a81-94ff-35917396bdfa[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n 10 --> 6a65ee93-3a2e-4a81-94ff-35917396bdfa;\n style 6a65ee93-3a2e-4a81-94ff-35917396bdfa stroke:#2c3143,stroke-width:4px;\n 11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n 7 -->|outfile| 11;\n 2 -->|out_file1| 11;\n b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n 11 --> b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2;\n style b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2 stroke:#2c3143,stroke-width:4px;\n 12[\"Select\"];\n 9 -->|output| 12;\n 13[\"Select\"];\n 9 -->|output| 13;\n 14[\"Select\"];\n 9 -->|output| 14;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 3: Functional Information",
"outputs": [
{
@@ -456902,7 +418678,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGene Family abundance\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nPathway abundance\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Cut\"];\n 0 -->|output| 3;\n 4[\"Renormalize\"];\n 1 -->|output| 4;\n 5[\"Regroup\"];\n 1 -->|output| 5;\n 6[\"Renormalize\"];\n 2 -->|output| 6;\n 7[\"Replace\"];\n 4 -->|output| 7;\n 8[\"Rename features\"];\n 5 -->|output| 8;\n 9[\"Split a HUMAnN table\"];\n 5 -->|output| 9;\n 7aba96f3-1648-4126-8e58-ca10cbd2e46d[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n 9 --> 7aba96f3-1648-4126-8e58-ca10cbd2e46d;\n style 7aba96f3-1648-4126-8e58-ca10cbd2e46d stroke:#2c3143,stroke-width:4px;\n 2c36dc33-5981-4b2c-b615-a1677002e007[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n 9 --> 2c36dc33-5981-4b2c-b615-a1677002e007;\n style 2c36dc33-5981-4b2c-b615-a1677002e007 stroke:#2c3143,stroke-width:4px;\n 10[\"Unpack pathway abundances\"];\n 4 -->|output| 10;\n 6 -->|output| 10;\n 11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n 7 -->|outfile| 11;\n 3 -->|out_file1| 11;\n 46161015-b2db-4241-846e-27dd803b0fb3[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n 11 --> 46161015-b2db-4241-846e-27dd803b0fb3;\n style 46161015-b2db-4241-846e-27dd803b0fb3 stroke:#2c3143,stroke-width:4px;\n 12[\"Select\"];\n 8 -->|output| 12;\n 13[\"Select\"];\n 8 -->|output| 13;\n 14[\"Select\"];\n 8 -->|output| 14;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 3: Functional Information (quick)",
"outputs": [
{
@@ -457604,7 +419380,7 @@
"Understand the output files from LotuS2",
"Understand the structure of the mapping file needed by LotuS2 to link sample metadata to a pair of FASTQ files"
],
- "pageviews": 194,
+ "pageviews": 200,
"pub_date": "2024-09-30",
"questions": [
"What is the fungal community composition in a given soil sample?"
@@ -457672,6 +419448,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -457727,10 +419507,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -457777,11 +419553,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -457826,6 +419597,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -457878,10 +419653,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -457915,10 +419686,10 @@
"state": "inexact",
"versions": [
"2.21",
- "2.06+galaxy3",
- "2.09.2",
"2.06",
"2.28.1+galaxy0",
+ "2.06+galaxy3",
+ "2.09.2",
"2.09"
]
},
@@ -457934,10 +419705,6 @@
"state": "exact",
"version": "2.32+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -457989,8 +419756,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 117,
- "visitors": 148,
+ "visit_duration": 112,
+ "visitors": 154,
"workflows": [
{
"creators": [
@@ -458116,7 +419883,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMapping tsv\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nsdm Options txt\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"LotuS2\"];\n 2 -->|output| 3;\n 0 -->|output| 3;\n 1 -->|output| 3;\n 7ff13687-fb95-4b54-8b5c-4c916500dfed[\"Output\\nOTU Table\"];\n 3 --> 7ff13687-fb95-4b54-8b5c-4c916500dfed;\n style 7ff13687-fb95-4b54-8b5c-4c916500dfed stroke:#2c3143,stroke-width:4px;\n b3413904-3319-4fa0-8c17-2c4757af5b8c[\"Output\\nOTU fasta\"];\n 3 --> b3413904-3319-4fa0-8c17-2c4757af5b8c;\n style b3413904-3319-4fa0-8c17-2c4757af5b8c stroke:#2c3143,stroke-width:4px;\n 11ad8056-9572-428a-a3b2-5ceec0fa186e[\"Output\\nComplete Output Zip\"];\n 3 --> 11ad8056-9572-428a-a3b2-5ceec0fa186e;\n style 11ad8056-9572-428a-a3b2-5ceec0fa186e stroke:#2c3143,stroke-width:4px;\n 21d55970-8b95-4dca-9b46-e7c65340ce84[\"Output\\nOTU Phylogenetic Tree\"];\n 3 --> 21d55970-8b95-4dca-9b46-e7c65340ce84;\n style 21d55970-8b95-4dca-9b46-e7c65340ce84 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'",
"outputs": [
{
@@ -458526,12 +420293,12 @@
"topic_0080"
],
"edam_operation": [
+ "Phylogenetic tree analysis",
+ "Aggregation",
"Visualisation",
+ "Taxonomic classification",
"Nucleic acid sequence analysis",
- "Aggregation",
- "Statistical calculation",
- "Phylogenetic tree analysis",
- "Taxonomic classification"
+ "Statistical calculation"
],
"edam_topic": [
"Metagenomics",
@@ -458547,7 +420314,6 @@
"hands_on": true,
"id": "microbiome/taxonomic-profiling",
"inexact_supported_servers": [
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"js_requirements": {
@@ -458571,7 +420337,7 @@
"Apply Krona and Pavian to visualize results of assignment and understand the output",
"Identify taxonomic classification tool that fits best depending on their data"
],
- "pageviews": 7752,
+ "pageviews": 7899,
"pub_date": "2023-05-03",
"questions": [
"Which species (or genera, families, ...) are present in my sample?",
@@ -458600,15 +420366,15 @@
],
"short_id": "T00395",
"short_tools": [
- "metaphlan",
- "__UNZIP_COLLECTION__",
- "kraken_biom",
+ "kraken2",
"interactive_tool_pavian",
- "interactive_tool_phinch",
- "taxonomy_krona_chart",
+ "kraken_biom",
"est_abundance",
- "kraken2",
- "krakentools_kreport2krona"
+ "metaphlan",
+ "interactive_tool_phinch",
+ "krakentools_kreport2krona",
+ "__UNZIP_COLLECTION__",
+ "taxonomy_krona_chart"
],
"slides": false,
"slides_recordings": false,
@@ -458622,11 +420388,6 @@
}
],
"inexact": [
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -458656,6 +420417,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -458711,10 +420476,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -458761,11 +420522,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -458810,6 +420566,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -458862,10 +420622,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -458906,10 +420662,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -458952,6 +420704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459004,10 +420760,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459048,10 +420800,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -459094,6 +420842,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459146,10 +420898,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459190,10 +420938,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -459236,6 +420980,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459298,10 +421046,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459352,11 +421096,6 @@
"state": "exact",
"version": "2.7.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -459402,6 +421141,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459457,10 +421200,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459510,11 +421249,6 @@
"state": "exact",
"version": "2.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -459562,6 +421296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459597,8 +421335,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.5+galaxy0",
- "2.6.1+galaxy0"
+ "2.6.1+galaxy0",
+ "2.5+galaxy0"
]
},
{
@@ -459621,10 +421359,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459669,15 +421403,6 @@
"state": "exact",
"version": "2.7+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.0+galaxy0",
- "2.8+galaxy0",
- "2.9+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -459732,6 +421457,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459786,10 +421515,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459823,8 +421548,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -459837,11 +421562,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -459887,6 +421607,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -459940,10 +421664,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -459986,11 +421706,6 @@
"state": "exact",
"version": "1.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -460035,6 +421750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -460094,10 +421813,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -460142,14 +421857,6 @@
"state": "exact",
"version": "1.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.2+galaxy1",
- "1.2+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -460194,6 +421901,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -460218,8 +421929,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2"
+ "4.1.1+galaxy2",
+ "4.1.1+galaxy1"
]
},
{
@@ -460254,10 +421965,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -460303,18 +422010,6 @@
"state": "exact",
"version": "4.0.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1.1+galaxy1",
- "4.1.1+galaxy2",
- "4.1.1+galaxy3",
- "4.0.6+galaxy3",
- "4.0.6+galaxy2",
- "4.1.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -460380,8 +422075,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 123,
- "visitors": 5642,
+ "visit_duration": 121,
+ "visitors": 5760,
"workflows": [
{
"creators": [
@@ -460398,7 +422093,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw-reads\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmetadata\"]\n 2[label=\"Unzip collection\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Kraken2\"]\n 0 -> 3 [label=\"output\"]\n ke2cffd0ae34244aa9637f8184ac72856[color=lightseagreen,label=\"Output\\nkraken_report\"]\n 3 -> ke2cffd0ae34244aa9637f8184ac72856\n 4[label=\"MetaPhlAn\"]\n 2 -> 4 [label=\"forward\"]\n 2 -> 4 [label=\"reverse\"]\n kdfd956c88e9f4878a27932df051c4c2a[color=lightseagreen,label=\"Output\\nmetaphlan_output\"]\n 4 -> kdfd956c88e9f4878a27932df051c4c2a\n 5[label=\"Krakentools: Convert kraken report file\"]\n 3 -> 5 [label=\"report_output\"]\n k324f53c0be2f40ecaa588b582545b161[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n 5 -> k324f53c0be2f40ecaa588b582545b161\n 6[label=\"Kraken-biom\"]\n 3 -> 6 [label=\"report_output\"]\n 1 -> 6 [label=\"output\"]\n 7[label=\"Pavian\"]\n 3 -> 7 [label=\"report_output\"]\n 8[label=\"Estimate Abundance at Taxonomic Level\"]\n 3 -> 8 [label=\"report_output\"]\n 9[label=\"Krona pie chart\"]\n 4 -> 9 [label=\"krona_output_file\"]\n 10[label=\"Krona pie chart\"]\n 5 -> 10 [label=\"output\"]\n 11[label=\"Phinch Visualisation\"]\n 6 -> 11 [label=\"biomOutput\"]\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw-reads\"]\n 1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmetadata\"]\n 2[label=\"Unzip collection\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"Kraken2\"]\n 0 -> 3 [label=\"output\"]\n kf0c347437c5b465a887f8f7e2cc854f3[color=lightseagreen,label=\"Output\\nkraken_report\"]\n 3 -> kf0c347437c5b465a887f8f7e2cc854f3\n 4[label=\"MetaPhlAn\"]\n 2 -> 4 [label=\"forward\"]\n 2 -> 4 [label=\"reverse\"]\n k2405fad5c770400aaa73f9d1f381224c[color=lightseagreen,label=\"Output\\nmetaphlan_output\"]\n 4 -> k2405fad5c770400aaa73f9d1f381224c\n 5[label=\"Krakentools: Convert kraken report file\"]\n 3 -> 5 [label=\"report_output\"]\n kd1ec0020964a4d5b9fe0a7ef1a9f668d[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n 5 -> kd1ec0020964a4d5b9fe0a7ef1a9f668d\n 6[label=\"Kraken-biom\"]\n 3 -> 6 [label=\"report_output\"]\n 1 -> 6 [label=\"output\"]\n 7[label=\"Pavian\"]\n 3 -> 7 [label=\"report_output\"]\n 8[label=\"Estimate Abundance at Taxonomic Level\"]\n 3 -> 8 [label=\"report_output\"]\n 9[label=\"Krona pie chart\"]\n 4 -> 9 [label=\"krona_output_file\"]\n 10[label=\"Krona pie chart\"]\n 5 -> 10 [label=\"output\"]\n 11[label=\"Phinch Visualisation\"]\n 6 -> 11 [label=\"biomOutput\"]\n}",
"history": [
{
"hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -460465,8 +422160,8 @@
}
],
"license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nraw-reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Unzip collection\"];\n 0 -->|output| 2;\n 3[\"Kraken2\"];\n 0 -->|output| 3;\n e2cffd0a-e342-44aa-9637-f8184ac72856[\"Output\\nkraken_report\"];\n 3 --> e2cffd0a-e342-44aa-9637-f8184ac72856;\n style e2cffd0a-e342-44aa-9637-f8184ac72856 stroke:#2c3143,stroke-width:4px;\n 4[\"MetaPhlAn\"];\n 2 -->|forward| 4;\n 2 -->|reverse| 4;\n dfd956c8-8e9f-4878-a279-32df051c4c2a[\"Output\\nmetaphlan_output\"];\n 4 --> dfd956c8-8e9f-4878-a279-32df051c4c2a;\n style dfd956c8-8e9f-4878-a279-32df051c4c2a stroke:#2c3143,stroke-width:4px;\n 5[\"Krakentools: Convert kraken report file\"];\n 3 -->|report_output| 5;\n 324f53c0-be2f-40ec-aa58-8b582545b161[\"Output\\nkrakentool_report\"];\n 5 --> 324f53c0-be2f-40ec-aa58-8b582545b161;\n style 324f53c0-be2f-40ec-aa58-8b582545b161 stroke:#2c3143,stroke-width:4px;\n 6[\"Kraken-biom\"];\n 3 -->|report_output| 6;\n 1 -->|output| 6;\n 7[\"Pavian\"];\n 3 -->|report_output| 7;\n 8[\"Estimate Abundance at Taxonomic Level\"];\n 3 -->|report_output| 8;\n 9[\"Krona pie chart\"];\n 4 -->|krona_output_file| 9;\n 10[\"Krona pie chart\"];\n 5 -->|output| 10;\n 11[\"Phinch Visualisation\"];\n 6 -->|biomOutput| 11;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nraw-reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Unzip collection\"];\n 0 -->|output| 2;\n 3[\"Kraken2\"];\n 0 -->|output| 3;\n f0c34743-7c5b-465a-887f-8f7e2cc854f3[\"Output\\nkraken_report\"];\n 3 --> f0c34743-7c5b-465a-887f-8f7e2cc854f3;\n style f0c34743-7c5b-465a-887f-8f7e2cc854f3 stroke:#2c3143,stroke-width:4px;\n 4[\"MetaPhlAn\"];\n 2 -->|forward| 4;\n 2 -->|reverse| 4;\n 2405fad5-c770-400a-aa73-f9d1f381224c[\"Output\\nmetaphlan_output\"];\n 4 --> 2405fad5-c770-400a-aa73-f9d1f381224c;\n style 2405fad5-c770-400a-aa73-f9d1f381224c stroke:#2c3143,stroke-width:4px;\n 5[\"Krakentools: Convert kraken report file\"];\n 3 -->|report_output| 5;\n d1ec0020-964a-4d5b-9fe0-a7ef1a9f668d[\"Output\\nkrakentool_report\"];\n 5 --> d1ec0020-964a-4d5b-9fe0-a7ef1a9f668d;\n style d1ec0020-964a-4d5b-9fe0-a7ef1a9f668d stroke:#2c3143,stroke-width:4px;\n 6[\"Kraken-biom\"];\n 3 -->|report_output| 6;\n 1 -->|output| 6;\n 7[\"Pavian\"];\n 3 -->|report_output| 7;\n 8[\"Estimate Abundance at Taxonomic Level\"];\n 3 -->|report_output| 8;\n 9[\"Krona pie chart\"];\n 4 -->|krona_output_file| 9;\n 10[\"Krona pie chart\"];\n 5 -->|output| 10;\n 11[\"Phinch Visualisation\"];\n 6 -->|biomOutput| 11;",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Taxonomic Profiling and Visualization of Metagenomic Data",
"outputs": [
{
@@ -460514,7 +422209,7 @@
{
"label": "kraken_report",
"output_name": "report_output",
- "uuid": "e2cffd0a-e342-44aa-9637-f8184ac72856"
+ "uuid": "f0c34743-7c5b-465a-887f-8f7e2cc854f3"
}
]
},
@@ -460584,7 +422279,7 @@
{
"label": "metaphlan_output",
"output_name": "output_file",
- "uuid": "dfd956c8-8e9f-4878-a279-32df051c4c2a"
+ "uuid": "2405fad5-c770-400a-aa73-f9d1f381224c"
}
]
},
@@ -460629,7 +422324,7 @@
{
"label": "krakentool_report",
"output_name": "output",
- "uuid": "324f53c0-be2f-40ec-aa58-8b582545b161"
+ "uuid": "d1ec0020-964a-4d5b-9fe0-a7ef1a9f668d"
}
]
}
@@ -460997,23 +422692,23 @@
],
"edam_operation": [
"Visualisation",
- "Data handling",
- "Variant calling",
- "Sequencing quality control",
- "Read pre-processing",
- "Sequence alignment analysis",
+ "Sequence trimming",
+ "Genome assembly",
"Sequence assembly validation",
- "Sequence file editing",
+ "Sequence assembly visualisation",
"Statistical calculation",
- "Genome assembly",
+ "Sequencing quality control",
"Formatting",
- "Primer removal",
"Sequence composition calculation",
- "Sequence assembly visualisation",
- "Read mapping",
- "Sequence trimming",
+ "Variant calling",
+ "Sequence file editing",
"Sequence contamination filtering",
- "Local alignment"
+ "Primer removal",
+ "Data handling",
+ "Local alignment",
+ "Sequence alignment analysis",
+ "Read mapping",
+ "Read pre-processing"
],
"edam_topic": [
"Metagenomics",
@@ -461053,7 +422748,7 @@
"Apply appropriate tools for analyzing the quality of metagenomic assembly",
"Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
],
- "pageviews": 3076,
+ "pageviews": 3131,
"pub_date": "2022-12-05",
"questions": [
"Why metagenomic data should be assembled?",
@@ -461085,24 +422780,24 @@
],
"short_id": "T00386",
"short_tools": [
- "fastqc",
- "collection_column_join",
- "bg_uniq",
- "tp_cat",
- "bowtie2",
+ "bandage_info",
+ "bandage_image",
"megahit",
- "cutadapt",
- "random_lines1",
"megahit_contig2fastg",
+ "metaspades",
"ngsutils_bam_filter",
- "filter_tabular",
- "bandage_info",
"quast",
+ "tp_cat",
+ "fastqc",
+ "bg_uniq",
+ "cutadapt",
+ "filter_tabular",
+ "random_lines1",
"seqtk_subseq",
- "metaspades",
- "bamtools",
"coverm_contig",
- "bandage_image"
+ "collection_column_join",
+ "bamtools",
+ "bowtie2"
],
"slides": false,
"slides_recordings": false,
@@ -461144,6 +422839,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -461199,10 +422898,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -461249,11 +422944,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -461298,6 +422988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -461350,10 +423044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -461394,10 +423084,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -461440,6 +423126,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -461494,10 +423184,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -461546,11 +423232,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -461596,6 +423277,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -461649,10 +423334,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -461696,11 +423377,6 @@
"state": "exact",
"version": "0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -461743,6 +423419,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -461798,10 +423478,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -461837,9 +423513,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.0.1",
+ "2.4.0.0",
"2.4.0",
- "2.4.0.0"
+ "0.0.1"
]
},
{
@@ -461854,11 +423530,6 @@
"state": "exact",
"version": "2.5.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -461906,6 +423577,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -461940,9 +423615,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -461966,10 +423641,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -462005,13 +423676,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -462020,12 +423691,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -462034,11 +423705,6 @@
"state": "exact",
"version": "2.4.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.5+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -462084,6 +423750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -462108,9 +423778,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -462122,9 +423792,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -462148,10 +423818,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -462187,13 +423853,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -462207,17 +423873,12 @@
"state": "exact",
"version": "2.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.4.5+galaxy1",
"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -462264,6 +423925,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -462321,10 +423986,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -462350,8 +424011,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -462375,12 +424036,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -462390,9 +424051,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -462403,11 +424064,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -462453,6 +424109,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -462514,10 +424174,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -462556,193 +424212,183 @@
"versions": [
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"0.8.1+galaxy1",
- "0.8.1+galaxy0",
- "0.8.1+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2022.09+galaxy4"
- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.8.1+galaxy4"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy4"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "2022.09+galaxy4",
- "0.8.1+galaxy3",
- "0.8.1+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "0.8.1+galaxy4"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "0.8.1+galaxy4"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
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- "version": "0.8.1+galaxy4"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
- },
- {
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
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- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "0.8.1+galaxy2"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "inexact",
- "versions": [
- "0.8.1+galaxy1"
- ]
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
- "2022.09+galaxy2",
- "0.8.1+galaxy1",
- "0.8.1+galaxy0"
- ]
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "0.8.1+galaxy2"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
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- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
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- "0.8.1+galaxy1",
- "0.8.1+galaxy0"
+ "0.8.1+galaxy0",
+ "0.8.1+galaxy2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2022.09+galaxy2"
+ "2022.09+galaxy4"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "0.8.1+galaxy4"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "2022.09+galaxy4",
+ "0.8.1+galaxy3",
+ "0.8.1+galaxy2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.8.1+galaxy4"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "0.8.1+galaxy4"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.8.1+galaxy4"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
"version": "0.8.1+galaxy2"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "inexact",
+ "versions": [
+ "0.8.1+galaxy1"
+ ]
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "2022.09+galaxy2",
+ "0.8.1+galaxy1",
+ "0.8.1+galaxy0"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "0.8.1+galaxy2"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.8.1+galaxy0+galaxy0",
+ "0.8.1+galaxy1",
+ "0.8.1+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2022.09+galaxy2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.8.1+galaxy2"
},
@@ -462791,6 +424437,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -462844,10 +424494,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -462892,11 +424538,6 @@
"state": "exact",
"version": "0.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -462942,6 +424583,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -462995,10 +424640,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -463044,14 +424685,6 @@
"state": "exact",
"version": "0.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.7.0+galaxy0",
- "0.6.1+galaxy3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -463094,6 +424727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463152,10 +424789,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -463205,10 +424838,6 @@
"state": "exact",
"version": "2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -463254,6 +424883,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463313,10 +424946,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -463370,11 +424999,6 @@
"state": "exact",
"version": "1.2.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -463420,6 +425044,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463473,10 +425101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -463520,11 +425144,6 @@
"state": "exact",
"version": "1.1.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -463570,6 +425189,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463625,10 +425248,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -463678,13 +425297,6 @@
"1.1.3+galaxy1"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.3+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -463736,6 +425348,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463788,10 +425404,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -463835,11 +425447,6 @@
"state": "exact",
"version": "0.5.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.9"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -463885,6 +425492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -463909,8 +425520,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
- "5.2.0+galaxy1"
+ "5.2.0+galaxy1",
+ "5.0.2+galaxy0"
]
},
{
@@ -463942,10 +425553,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -463984,23 +425591,23 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "5.0.2+galaxy0",
"5.2.0+galaxy1",
+ "5.0.2+galaxy0",
"5.0.2+galaxy1",
"5.0.2+galaxy4",
- "5.0.2",
"4.1",
+ "5.0.2",
+ "5.0.2+galaxy2",
"5.0.2+galaxy5",
- "5.0.2+galaxy3",
- "5.0.2+galaxy2"
+ "5.0.2+galaxy3"
]
},
{
@@ -464008,11 +425615,6 @@
"state": "exact",
"version": "5.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -464058,6 +425660,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -464112,10 +425718,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -464152,8 +425754,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -464166,11 +425768,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -464216,6 +425813,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -464270,10 +425871,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -464320,11 +425917,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -464371,6 +425963,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -464407,8 +426003,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -464431,10 +426027,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -464477,8 +426069,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -464493,11 +426085,6 @@
"state": "exact",
"version": "4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -464545,6 +426132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -464598,10 +426189,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -464651,11 +426238,6 @@
"state": "exact",
"version": "3.15.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.15.4+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -464730,8 +426312,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 177,
- "visitors": 2189,
+ "visit_duration": 175,
+ "visitors": 2230,
"workflows": [
{
"creators": [],
@@ -464788,7 +426370,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"metaSPAdes\"];\n 0 -->|output| 1;\n 833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n 1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n 10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n 1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n 1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n 1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n 2[\"MEGAHIT\"];\n 0 -->|output| 2;\n 3[\"Bowtie2\"];\n 0 -->|output| 3;\n 2 -->|output| 3;\n 4[\"megahit contig2fastg\"];\n 2 -->|output| 4;\n 5[\"Quast\"];\n 2 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Bandage Image\"];\n 4 -->|fastg| 6;\n 7[\"Bandage Info\"];\n 4 -->|fastg| 7;\n 8[\"Column join\"];\n 7 -->|outfile| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Metagenomics assembly tutorial workflow",
"outputs": [
{
@@ -465380,7 +426962,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Cutadapt\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"MEGAHIT\"];\n 2 -->|out1| 3;\n 2 -->|out2| 3;\n 4[\"Bowtie2\"];\n 2 -->|out1| 4;\n 2 -->|out2| 4;\n 3 -->|output| 4;\n 5[\"BAM filter\"];\n 4 -->|output| 5;\n 6[\"BAM filter\"];\n 4 -->|output| 6;\n 7[\"Convert, Merge, Randomize\"];\n 5 -->|outfile| 7;\n 8[\"Convert, Merge, Randomize\"];\n 6 -->|outfile| 8;\n 9[\"Select random lines\"];\n 7 -->|out_file1| 9;\n 10[\"Select random lines\"];\n 8 -->|out_file1| 10;\n 11[\"Filter Tabular\"];\n 9 -->|out_file1| 11;\n 12[\"Filter Tabular\"];\n 10 -->|out_file1| 12;\n 13[\"Unique\"];\n 11 -->|output| 13;\n 14[\"Unique\"];\n 12 -->|output| 14;\n 15[\"Concatenate datasets\"];\n 13 -->|outfile| 15;\n 14 -->|outfile| 15;\n 16[\"seqtk_subseq\"];\n 2 -->|out1| 16;\n 15 -->|out_file1| 16;\n 17[\"seqtk_subseq\"];\n 2 -->|out2| 17;\n 15 -->|out_file1| 17;\n 18[\"FastQC\"];\n 16 -->|default| 18;\n 19[\"FastQC\"];\n 17 -->|default| 19;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "workflow-generate-dataset-for-assembly-tutorial",
"outputs": [
{
@@ -466480,16 +428062,16 @@
],
"dir": "topics/microbiome/tutorials/clinical-mp-2-discovery",
"edam_operation": [
- "Imputation",
- "Visualisation",
"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Formatting",
"Filtering",
- "Heat map generation",
+ "Visualisation",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
+ "Formatting",
"Protein quantification",
- "Principal component plotting"
+ "Heat map generation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -466522,14 +428104,14 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Perform Database searching using two algorithms",
"Extract confident peptides and proteins",
"Generate a microbial peptide panel for verification"
],
"pageviews": 0,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
"How to perform database searching?",
"How to extract microbial and Human protein and peptide sequences from the results"
@@ -466561,23 +428143,23 @@
],
"short_id": "T00461",
"short_tools": [
- "Grep1",
- "search_gui",
- "fasta_merge_files_and_filter_unique_sequences",
- "dbbuilder",
- "tp_cat",
- "fasta_cli",
- "Remove beginning1",
- "msconvert",
"Filter1",
- "maxquant",
+ "Cut1",
+ "dbbuilder",
"ident_params",
- "fasta2tab",
- "peptide_shaker",
- "filter_tabular",
"query_tabular",
+ "fasta_merge_files_and_filter_unique_sequences",
"Grouping1",
- "Cut1"
+ "tp_cat",
+ "fasta2tab",
+ "msconvert",
+ "Grep1",
+ "Remove beginning1",
+ "filter_tabular",
+ "search_gui",
+ "maxquant",
+ "fasta_cli",
+ "peptide_shaker"
],
"slides": false,
"slides_recordings": false,
@@ -466629,6 +428211,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -466684,10 +428270,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -466734,11 +428316,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -466783,6 +428360,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -466835,10 +428416,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -466879,10 +428456,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -466925,6 +428498,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -466977,10 +428554,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -467021,10 +428594,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -467067,6 +428636,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -467119,10 +428692,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -467163,10 +428732,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -467209,6 +428774,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -467261,10 +428830,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -467305,10 +428870,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -467351,6 +428912,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -467403,10 +428968,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -467447,10 +429008,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -467493,6 +429050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -467547,10 +429108,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -467599,11 +429156,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -467649,6 +429201,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -467704,10 +429260,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -467754,11 +429306,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -467804,6 +429351,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -467856,10 +429407,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -467905,11 +429452,6 @@
"state": "exact",
"version": "0.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -467955,6 +429497,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468008,10 +429554,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -468056,11 +429598,6 @@
"state": "exact",
"version": "1.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -468106,6 +429643,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468158,10 +429699,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468205,10 +429742,6 @@
"state": "exact",
"version": "2.0.3.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -468256,6 +429789,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468308,10 +429845,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468344,8 +429877,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.19052.1",
- "3.0.19052.0"
+ "3.0.19052.0",
+ "3.0.19052.1"
]
},
{
@@ -468358,11 +429891,6 @@
"state": "exact",
"version": "3.0.20287.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.20287.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -468411,6 +429939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468463,10 +429995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468509,11 +430037,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -468558,6 +430081,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468610,10 +430137,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468656,11 +430179,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -468705,6 +430223,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468757,10 +430279,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468807,11 +430325,6 @@
"state": "exact",
"version": "2.0.33+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.33+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -468860,6 +430373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -468912,10 +430429,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -468962,11 +430475,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -469014,6 +430522,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -469068,10 +430580,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -469118,10 +430626,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -469167,6 +430671,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -469225,10 +430733,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -469274,11 +430778,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -469452,7 +430951,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Identification Parameters: PAR file\"];\n 2[\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Human SwissProt reviewed only\"];\n e0de9f90-a710-4b55-af62-41ba1c2d8e1f[\"Output\\nHuman SwissProt (reviewed only)\"];\n 3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;\n style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;\n 4[\"Contaminants cRAP\"];\n 5[\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"];\n 0 -->|output| 6;\n 7[\"msconvert\"];\n 2 -->|output| 7;\n 8[\"Human SwissProt+cRAP\"];\n 3 -->|output_database| 8;\n 4 -->|output_database| 8;\n 2f14902f-b005-4c08-b6d1-6d7ee0b4b199[\"Output\\nHuman SwissProt+cRAP\"];\n 8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;\n style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;\n 9[\"MaxQuant\"];\n 0 -->|output| 9;\n 2 -->|output| 9;\n 5 -->|output| 9;\n 10[\"Search GUI\"];\n 6 -->|input_database_concatenated_target_decoy| 10;\n 1 -->|Identification_Parameters_File| 10;\n 7 -->|output| 10;\n 11[\"FASTA-to-Tabular\"];\n 8 -->|output| 11;\n 12[\"Select microbial peptides MQ\"];\n 9 -->|peptides| 12;\n d7718bab-9e75-4729-bfb6-03bc3112a0e2[\"Output\\nSelect microbial peptides (MQ)\"];\n 12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;\n style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;\n 13[\"Peptide Shaker\"];\n 10 -->|searchgui_results| 13;\n 14[\"Filter Tabular\"];\n 11 -->|output| 14;\n 15[\"MQ Peptide Sequences\"];\n 12 -->|out_file1| 15;\n 16[\"Select microbial peptides SGPS\"];\n 13 -->|output_peptides| 16;\n 14fd9080-df92-4c61-b1f1-3f700a166700[\"Output\\nSelect microbial peptides (SGPS)\"];\n 16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;\n style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;\n 17[\"Select microbial PSMs\"];\n 13 -->|output_psm| 17;\n 18[\"Remove beginning\"];\n 15 -->|out_file1| 18;\n 19[\"Filter confident microbial peptides\"];\n 16 -->|out_file1| 19;\n 1c6c953f-d192-4953-938a-9f401315bc0d[\"Output\\nFilter confident microbial peptides\"];\n 19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;\n style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;\n 20[\"Filter confident microbial PSMs\"];\n 17 -->|out_file1| 20;\n d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2[\"Output\\nFilter confident microbial PSMs\"];\n 20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;\n style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;\n 21[\"MQ Distinct Peptides\"];\n 18 -->|out_file1| 21;\n 07cae017-0b39-4065-b83e-b5f2e27fe740[\"Output\\nMQ Peptides\"];\n 21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;\n style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;\n 22[\"Query Tabular\"];\n 20 -->|out_file1| 22;\n 20 -->|out_file1| 22;\n 14 -->|output| 22;\n 23[\"Cut\"];\n 22 -->|output| 23;\n 24[\"SGPS Distinct Peptides\"];\n 23 -->|out_file1| 24;\n b6c61697-ff52-43c0-8fb4-765d7b4204cc[\"Output\\nSGPS Distinct Peptides\"];\n 24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;\n style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;\n 25[\"SGPS-MQ Peptides\"];\n 21 -->|out_file1| 25;\n 24 -->|out_file1| 25;\n a8c2de2e-e322-4830-9d28-2f79bf937013[\"Output\\nSGPS-MQ Peptides\"];\n 25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;\n style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;\n 26[\"Distinct Peptides\"];\n 25 -->|out_file1| 26;\n ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7[\"Output\\nDistinct Peptides\"];\n 26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;\n style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF2_Discovery-Workflow",
"outputs": [
{
@@ -470364,11 +431863,11 @@
],
"dir": "topics/microbiome/tutorials/clinical-mp-1-database-generation",
"edam_operation": [
- "Expression analysis",
+ "Target-Decoy",
+ "de Novo sequencing",
"Tag-based peptide identification",
"Protein identification",
- "Target-Decoy",
- "de Novo sequencing"
+ "Expression analysis"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -470401,14 +431900,14 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
"Downloading databases related to 16SrRNA data",
"For better identification results, combine host and microbial proteins.",
"Reduced database provides better FDR stats."
],
- "pageviews": 1,
- "pub_date": "2024-12-09",
+ "pageviews": 0,
+ "pub_date": "2024-12-13",
"questions": [
"Why do we need to generate a customized database for metaproteomics research?",
"How do we reduce the size of the database?"
@@ -470440,10 +431939,10 @@
],
"short_id": "T00460",
"short_tools": [
- "metanovo",
- "dbbuilder",
"fasta_merge_files_and_filter_unique_sequences",
- "uniprotxml_downloader"
+ "dbbuilder",
+ "uniprotxml_downloader",
+ "metanovo"
],
"slides": false,
"slides_recordings": false,
@@ -470496,6 +431995,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -470551,10 +432054,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -470601,11 +432100,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -470650,6 +432144,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -470702,10 +432200,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -470751,11 +432245,6 @@
"state": "exact",
"version": "0.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -470801,6 +432290,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -470854,10 +432347,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -470902,11 +432391,6 @@
"state": "exact",
"version": "1.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -470952,6 +432436,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -471004,10 +432492,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -471050,10 +432534,6 @@
"state": "exact",
"version": "1.9.4+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -471098,6 +432578,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -471150,10 +432634,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -471196,10 +432676,6 @@
"state": "exact",
"version": "2.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -471260,7 +432736,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 0,
- "visitors": 1,
+ "visitors": 0,
"workflows": [
{
"creators": [
@@ -471391,7 +432867,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Human UniProt Microbial Proteins cRAP for MetaNovo\"];\n 0 -->|output| 4;\n 2 -->|output| 4;\n 3 -->|output| 4;\n 286f5bd4-fb0d-4649-8dac-f191acc72722[\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"];\n 4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;\n style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;\n 5[\"MetaNovo\"];\n 4 -->|output| 5;\n 1 -->|output| 5;\n 6[\"FASTA Merge Files and Filter Unique Sequences\"];\n 0 -->|output| 6;\n 5 -->|output_fasta| 6;\n 3 -->|output| 6;\n de57cd9d-ac05-4397-9d44-e65620913447[\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"];\n 6 --> de57cd9d-ac05-4397-9d44-e65620913447;\n style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF1_Database_Generation_Workflow",
"outputs": [
{
@@ -471757,20 +433233,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json",
- "contributions": {
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- "shiltemann"
- ],
- "reviewing": [
- "shiltemann",
- "bebatut",
- "bgruening",
- "willemdek11",
- "hexylena",
- "mmiladi"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -471815,142 +433277,6 @@
"orcid": "0000-0003-3803-468X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "nl",
- "id": "willemdek11",
- "joined": "2018-09",
- "name": "Willem de Koning",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willemdek11/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willemdek11.json"
- },
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- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "id": "mmiladi",
- "name": "mmiladi",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mmiladi/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mmiladi.json"
}
],
"dir": "topics/microbiome/tutorials/plasmid-metagenomics-nanopore",
@@ -471964,15 +433290,15 @@
"topic_4013"
],
"edam_operation": [
- "Scatter plot plotting",
- "Genome assembly",
"Pairwise sequence alignment",
+ "Genome assembly",
+ "Sequence assembly visualisation",
+ "Aggregation",
"Mapping assembly",
- "Box-Whisker plot plotting",
+ "Sequence analysis",
+ "Scatter plot plotting",
"De-novo assembly",
- "Aggregation",
- "Sequence assembly visualisation",
- "Sequence analysis"
+ "Box-Whisker plot plotting"
],
"edam_topic": [
"Metagenomic sequencing",
@@ -472017,7 +433343,7 @@
"Determine the structure of the genome(s)",
"Scan for antimicrobial resistance genes with Staramr"
],
- "pageviews": 2296,
+ "pageviews": 2546,
"pub_date": "2019-06-25",
"questions": [
"How do I assemble a genome with Nanopore data?",
@@ -472046,14 +433372,14 @@
],
"short_id": "T00394",
"short_tools": [
- "staramr_search",
- "nanoplot",
+ "PlasFlow",
"minimap2",
- "racon",
- "unicycler",
- "bandage_image",
"gfa_to_fa",
- "PlasFlow",
+ "bandage_image",
+ "unicycler",
+ "staramr_search",
+ "racon",
+ "nanoplot",
"miniasm"
],
"slides": false,
@@ -472117,6 +433443,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -472172,10 +433502,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -472222,11 +433548,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -472271,6 +433592,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -472304,8 +433629,8 @@
"state": "inexact",
"versions": [
"1.4.13",
- "1.4.20+galaxy0",
- "1.5.0+galaxy1"
+ "1.5.0+galaxy1",
+ "1.4.20+galaxy0"
]
},
{
@@ -472328,10 +433653,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -472375,14 +433696,6 @@
"state": "exact",
"version": "1.3.1.1"
},
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- "state": "inexact",
- "versions": [
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- "1.5.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -472433,6 +433746,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -472486,10 +433803,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -472522,8 +433835,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.1",
- "1.3.1.1"
+ "1.3.1.1",
+ "1.3.1"
]
},
{
@@ -472536,14 +433849,6 @@
"state": "exact",
"version": "1.4.13"
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- "state": "inexact",
- "versions": [
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- "1.5.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -472589,6 +433894,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -472613,8 +433922,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.8.1+galaxy0+galaxy0",
"0.8.1+galaxy4",
+ "0.8.1+galaxy0+galaxy0",
"2022.09+galaxy4"
]
},
@@ -472654,10 +433963,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -472707,16 +434012,6 @@
"state": "exact",
"version": "0.8.1+galaxy0"
},
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- "2022.09+galaxy4",
- "0.8.1+galaxy3",
- "0.8.1+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -472766,6 +434061,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -472790,8 +434089,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.8.1+galaxy0+galaxy0",
"0.8.1+galaxy4",
+ "0.8.1+galaxy0+galaxy0",
"2022.09+galaxy4"
]
},
@@ -472831,10 +434130,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -472884,11 +434179,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.8.1+galaxy2"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -472934,6 +434224,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -472986,10 +434280,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -473035,13 +434325,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.1.2"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -473096,6 +434379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473148,10 +434435,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -473197,13 +434480,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.1.2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -473249,6 +434525,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473281,8 +434561,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.3+galaxy0",
- "0.3+galaxy1"
+ "0.3+galaxy1",
+ "0.3+galaxy0"
]
},
{
@@ -473305,10 +434585,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -473354,19 +434630,12 @@
"state": "exact",
"version": "0.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.3_r179+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "0.3+galaxy0",
"0.3+galaxy1",
+ "0.3+galaxy0",
"0.3_r179+galaxy1",
"0.3_r179+galaxy0"
]
@@ -473411,6 +434680,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473464,10 +434737,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -473513,13 +434782,6 @@
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- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -473565,6 +434827,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473589,8 +434855,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
+ "2.28+galaxy0",
+ "2.24+galaxy0"
]
},
{
@@ -473602,8 +434868,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -473626,10 +434892,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -473678,20 +434940,6 @@
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- {
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- "state": "inexact",
- "versions": [
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- "2.28+galaxy0",
- "2.27+galaxy0",
- "2.12",
- "2.26+galaxy0",
- "2.23+galaxy0",
- "2.17+galaxy2",
- "2.22+galaxy0"
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{
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"state": "inexact",
@@ -473740,6 +434988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473764,8 +435016,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
+ "2.28+galaxy0",
+ "2.24+galaxy0"
]
},
{
@@ -473777,8 +435029,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -473801,10 +435053,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -473841,12 +435089,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -473861,11 +435109,6 @@
"state": "exact",
"version": "2.17+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.17+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -473914,6 +435157,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -473975,10 +435222,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -474027,18 +435270,6 @@
"state": "exact",
"version": "1.25.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.42.0+galaxy0",
- "1.43.0+galaxy0",
- "1.28.2+galaxy1",
- "1.41.0+galaxy0",
- "1.42.0+galaxy1",
- "1.36.2+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -474084,6 +435315,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474143,10 +435378,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -474195,11 +435426,6 @@
"state": "exact",
"version": "1.28.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -474245,6 +435471,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474298,10 +435528,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -474347,10 +435573,6 @@
"state": "exact",
"version": "1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -474398,6 +435620,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474453,10 +435679,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -474505,11 +435727,6 @@
"state": "exact",
"version": "0.4.7.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.7.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -474557,6 +435774,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474610,10 +435831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -474662,11 +435879,6 @@
"state": "exact",
"version": "0.4.8.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.8.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -474712,6 +435924,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474736,8 +435952,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.7.2+galaxy0",
"0.10.0+galaxy0",
+ "0.7.2+galaxy0",
"0.10.0+galaxy1"
]
},
@@ -474770,10 +435986,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -474820,15 +436032,6 @@
"state": "exact",
"version": "0.5.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.10.0+galaxy0",
- "0.10.0+galaxy1",
- "0.9.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -474847,13 +436050,13 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "0.7.2+galaxy0",
"0.10.0+galaxy0",
+ "0.7.2+galaxy0",
"0.10.0+galaxy1",
- "0.8.0+galaxy0",
"0.9.1+galaxy0",
- "0.7.1+galaxy2",
- "0.7.1+galaxy1"
+ "0.8.0+galaxy0",
+ "0.7.1+galaxy1",
+ "0.7.1+galaxy2"
]
},
{
@@ -474886,6 +436089,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -474910,8 +436117,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.7.2+galaxy0",
"0.10.0+galaxy0",
+ "0.7.2+galaxy0",
"0.10.0+galaxy1"
]
},
@@ -474924,10 +436131,10 @@
"state": "inexact",
"versions": [
"0.7.2+galaxy0",
+ "0.9.1+galaxy0",
"0.5.1",
- "0.2.1",
"0.8.0+galaxy0",
- "0.9.1+galaxy0"
+ "0.2.1"
]
},
{
@@ -474950,10 +436157,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -475002,15 +436205,6 @@
"state": "exact",
"version": "0.7.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.10.0+galaxy0",
- "0.10.0+galaxy1",
- "0.9.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -475083,8 +436277,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 230,
- "visitors": 1551,
+ "visit_duration": 212,
+ "visitors": 1734,
"workflows": [
{
"creators": [],
@@ -475130,7 +436324,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nPlasmids\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"NanoPlot\"];\n 0 -->|output| 1;\n 10[\"NanoPlot\"];\n 9 -->|out_fa| 10;\n 11[\"Map with minimap2\"];\n 0 -->|output| 11;\n 9 -->|out_fa| 11;\n 12[\"Racon\"];\n 9 -->|out_fa| 12;\n 11 -->|alignment_output| 12;\n 0 -->|output| 12;\n 2[\"Map with minimap2\"];\n 0 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Create assemblies with Unicycler\"];\n 0 -->|output| 3;\n 4[\"miniasm\"];\n 2 -->|alignment_output| 4;\n 0 -->|output| 4;\n 5[\"Bandage Image\"];\n 3 -->|assembly_graph| 5;\n 6[\"PlasFlow\"];\n 3 -->|assembly| 6;\n 7[\"staramr\"];\n 3 -->|assembly| 7;\n 8[\"Bandage Image\"];\n 4 -->|gfa| 8;\n 9[\"GFA to FASTA\"];\n 4 -->|gfa| 9;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Copy Of GTN Training - Antibiotic Resistance Detection",
"outputs": [],
"parent_id": "microbiome/plasmid-metagenomics-nanopore",
@@ -475544,11 +436738,11 @@
"topic_4038"
],
"edam_operation": [
- "Visualisation",
- "Analysis",
+ "Deposition",
"Variant calling",
+ "Visualisation",
"DNA barcoding",
- "Deposition"
+ "Analysis"
],
"edam_topic": [
"Microbial ecology",
@@ -475584,7 +436778,7 @@
"Compare the advantages of ASV-based methods over traditional OTU-based approaches in terms of accuracy and resolution",
"Assess the effectiveness of using phyloseq for exploring and visualizing ASV data to gain ecological and evolutionary insights"
],
- "pageviews": 2735,
+ "pageviews": 2807,
"pub_date": "2024-06-05",
"questions": [
"What are the primary steps involved in generating an ASV table using DADA2 from 16S rRNA gene sequencing data?",
@@ -475611,26 +436805,26 @@
],
"short_id": "T00441",
"short_tools": [
- "dada2_seqCounts",
- "__UNZIP_COLLECTION__",
- "dada2_assignTaxonomyAddspecies",
- "tp_replace_in_column",
- "tp_replace_in_line",
- "Add_a_column1",
- "Grouping1",
- "interactive_tool_phyloseq",
- "phyloseq_from_dada2",
- "dada2_makeSequenceTable",
"cat1",
"dada2_dada",
- "dada2_plotQualityProfile",
+ "dada2_filterAndTrim",
"tp_head_tool",
- "__SORTLIST__",
+ "collection_element_identifiers",
"dada2_mergePairs",
+ "tp_replace_in_line",
+ "tp_replace_in_column",
+ "Add_a_column1",
+ "interactive_tool_phyloseq",
+ "dada2_assignTaxonomyAddspecies",
"dada2_learnErrors",
- "collection_element_identifiers",
+ "dada2_makeSequenceTable",
+ "__SORTLIST__",
"dada2_removeBimeraDenovo",
- "dada2_filterAndTrim"
+ "Grouping1",
+ "dada2_seqCounts",
+ "phyloseq_from_dada2",
+ "__UNZIP_COLLECTION__",
+ "dada2_plotQualityProfile"
],
"slides": false,
"slides_recordings": false,
@@ -475672,6 +436866,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -475727,10 +436925,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -475777,11 +436971,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -475826,6 +437015,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -475878,10 +437071,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -475922,10 +437111,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -475968,6 +437153,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -476020,10 +437209,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -476064,10 +437249,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -476110,6 +437291,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -476162,10 +437347,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -476206,10 +437387,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -476252,6 +437429,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -476304,10 +437485,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -476348,10 +437525,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -476394,6 +437567,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -476446,10 +437623,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -476490,10 +437663,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -476536,6 +437705,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -476594,10 +437767,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -476647,11 +437816,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -476699,6 +437863,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -476757,10 +437925,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -476814,11 +437978,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -476869,6 +438028,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -476923,10 +438086,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -476973,11 +438132,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -477023,6 +438177,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477081,10 +438239,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -477120,8 +438274,8 @@
"versions": [
"1.1.2",
"1.1.0",
- "1.0.0",
- "1.1.1"
+ "1.1.1",
+ "1.0.0"
]
},
{
@@ -477137,11 +438291,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -477191,6 +438340,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477251,10 +438404,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -477288,9 +438437,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -477304,11 +438453,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -477354,6 +438498,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477408,10 +438556,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -477456,11 +438600,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -477506,6 +438645,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477544,9 +438687,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.12+galaxy1",
- "1.14+galaxy0"
+ "1.14+galaxy0",
+ "1.18+galaxy0"
]
},
{
@@ -477569,10 +438712,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -477620,17 +438759,12 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.14+galaxy0",
+ "1.18+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -477675,6 +438809,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477709,9 +438847,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.12+galaxy1",
- "1.14+galaxy0"
+ "1.14+galaxy0",
+ "1.18+galaxy0"
]
},
{
@@ -477734,10 +438872,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -477779,8 +438913,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.28+galaxy0",
- "1.20+galaxy0"
+ "1.20+galaxy0",
+ "1.28+galaxy0"
]
},
{
@@ -477788,17 +438922,12 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.14+galaxy0",
+ "1.18+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -477843,6 +438972,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -477905,10 +439038,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -477956,11 +439085,6 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -478011,6 +439135,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478069,10 +439197,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478123,11 +439247,6 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -478178,6 +439297,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478216,9 +439339,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
+ "1.14+galaxy0",
"1.12+galaxy1",
- "1.14+galaxy0"
+ "1.18+galaxy0"
]
},
{
@@ -478241,10 +439364,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478277,8 +439396,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -478292,17 +439411,12 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.14+galaxy0",
+ "1.18+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -478347,6 +439461,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478381,9 +439499,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
+ "1.14+galaxy0",
"1.12+galaxy1",
- "1.14+galaxy0"
+ "1.18+galaxy0"
]
},
{
@@ -478406,10 +439524,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478442,8 +439556,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -478451,8 +439565,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.20+galaxy0",
- "1.28+galaxy0"
+ "1.28+galaxy0",
+ "1.20+galaxy0"
]
},
{
@@ -478460,17 +439574,12 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.14+galaxy0",
+ "1.18+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -478515,6 +439624,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478553,9 +439666,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
- "1.18+galaxy0"
+ "1.18+galaxy0",
+ "1.12+galaxy1"
]
},
{
@@ -478578,10 +439691,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478614,8 +439723,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -478629,11 +439738,6 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -478684,6 +439788,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478718,9 +439826,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
- "1.18+galaxy0"
+ "1.18+galaxy0",
+ "1.12+galaxy1"
]
},
{
@@ -478743,10 +439851,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478779,8 +439883,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -478788,8 +439892,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.28+galaxy0",
- "1.20+galaxy0"
+ "1.20+galaxy0",
+ "1.28+galaxy0"
]
},
{
@@ -478797,11 +439901,6 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -478852,6 +439951,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -478890,9 +439993,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
+ "1.18+galaxy0",
"1.14+galaxy0",
- "1.18+galaxy0"
+ "1.12+galaxy1"
]
},
{
@@ -478915,10 +440018,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -478951,8 +440050,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -478966,17 +440065,12 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.14+galaxy0",
"1.18+galaxy0",
+ "1.14+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -479021,6 +440115,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -479055,9 +440153,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
+ "1.18+galaxy0",
"1.14+galaxy0",
- "1.18+galaxy0"
+ "1.12+galaxy1"
]
},
{
@@ -479080,10 +440178,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -479116,8 +440210,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.12+galaxy1",
"1.14+galaxy0",
+ "1.12+galaxy1",
"1.12+galaxy0"
]
},
@@ -479125,8 +440219,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.28+galaxy0",
- "1.20+galaxy0"
+ "1.20+galaxy0",
+ "1.28+galaxy0"
]
},
{
@@ -479134,17 +440228,12 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.14+galaxy0",
"1.18+galaxy0",
+ "1.14+galaxy0",
"1.20+galaxy0",
"1.16+galaxy0"
]
@@ -479189,6 +440278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -479252,10 +440345,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -479304,11 +440393,6 @@
"state": "exact",
"version": "1.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -479359,6 +440443,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -479418,10 +440506,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -479464,8 +440548,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.20+galaxy0",
- "1.28+galaxy0"
+ "1.28+galaxy0",
+ "1.20+galaxy0"
]
},
{
@@ -479473,11 +440557,6 @@
"state": "exact",
"version": "1.30.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.30.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -479528,6 +440607,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -479566,8 +440649,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.18+galaxy0",
"1.14+galaxy0",
+ "1.18+galaxy0",
"1.12+galaxy1"
]
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@@ -479591,10 +440674,6 @@
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]
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"1.12+galaxy1",
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+ "1.14+galaxy0"
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"1.18+galaxy0",
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]
@@ -480539,6 +441588,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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@@ -480592,10 +441645,6 @@
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{
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@@ -480640,11 +441689,6 @@
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{
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@@ -480730,8 +441774,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 121,
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+ "visit_duration": 119,
+ "visitors": 2059,
"workflows": [
{
"creators": [
@@ -480828,7 +441872,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nRaw reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nheader\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Sort collection\"];\n 0 -->|output| 2;\n 3[\"dada2: filterAndTrim\"];\n 2 -->|output| 3;\n 4[\"dada2: plotQualityProfile\"];\n 2 -->|output| 4;\n 5[\"Unzip collection\"];\n 3 -->|paired_output| 5;\n 6[\"dada2: plotQualityProfile\"];\n 3 -->|paired_output| 6;\n 7[\"dada2: learnErrors\"];\n 5 -->|forward| 7;\n 8[\"dada2: learnErrors\"];\n 5 -->|reverse| 8;\n 9[\"dada2: dada\"];\n 5 -->|forward| 9;\n 7 -->|errors| 9;\n 10[\"dada2: dada\"];\n 5 -->|reverse| 10;\n 8 -->|errors| 10;\n 11[\"dada2: mergePairs\"];\n 9 -->|data_collection| 11;\n 10 -->|data_collection| 11;\n 5 -->|forward| 11;\n 5 -->|reverse| 11;\n 12[\"Extract element identifiers\"];\n 11 -->|merged| 12;\n 13[\"dada2: makeSequenceTable\"];\n 11 -->|merged| 13;\n 3fd25979-39df-4698-bad1-aabfccbb7bd2[\"Output\\nsequence_table\"];\n 13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;\n style 3fd25979-39df-4698-bad1-aabfccbb7bd2 stroke:#2c3143,stroke-width:4px;\n 14[\"Replace Text\"];\n 12 -->|output| 14;\n 15[\"dada2: removeBimeraDenovo\"];\n 13 -->|stable| 15;\n 16[\"Select first\"];\n 14 -->|outfile| 16;\n 17[\"dada2: sequence counts\"];\n 3 -->|outtab| 17;\n 9 -->|data_collection| 17;\n 10 -->|data_collection| 17;\n 11 -->|merged| 17;\n 15 -->|stable_sequencetable| 17;\n c758f861-44bc-4208-b1f7-1f5106cb678e[\"Output\\nsequence_counts\"];\n 17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;\n style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;\n 18[\"dada2: assignTaxonomy and addSpecies\"];\n 15 -->|stable_sequencetable| 18;\n 904fe0a2-8329-45ca-8493-fc688fb216c3[\"Output\\ntaxons\"];\n 18 --> 904fe0a2-8329-45ca-8493-fc688fb216c3;\n style 904fe0a2-8329-45ca-8493-fc688fb216c3 stroke:#2c3143,stroke-width:4px;\n 19[\"Compute\"];\n 16 -->|outfile| 19;\n 20[\"Replace Text\"];\n 19 -->|out_file1| 20;\n 21[\"Concatenate datasets\"];\n 1 -->|output| 21;\n 20 -->|outfile| 21;\n 5479d320-3e82-47a9-a92b-6ed5959459cf[\"Output\\nmetada_table\"];\n 21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;\n style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;\n 22[\"Create phyloseq object\"];\n 21 -->|out_file1| 22;\n 15 -->|stable_sequencetable| 22;\n 18 -->|output| 22;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
"outputs": [
{
@@ -481157,14 +442201,14 @@
],
"dir": "topics/microbiome/tutorials/clinical-mp-4-quantitation",
"edam_operation": [
- "Imputation",
- "Visualisation",
"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Heat map generation",
+ "Visualisation",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
"Protein quantification",
- "Principal component plotting"
+ "Heat map generation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -481199,12 +442243,12 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
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],
"pageviews": 0,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
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],
@@ -481235,10 +442279,10 @@
],
"short_id": "T00463",
"short_tools": [
- "Grep1",
- "maxquant",
"Grouping1",
- "Cut1"
+ "Grep1",
+ "Cut1",
+ "maxquant"
],
"slides": false,
"slides_recordings": false,
@@ -481301,6 +442345,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -481356,10 +442404,6 @@
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"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -481406,11 +442450,6 @@
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{
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"url": "https://usegalaxy.no/",
@@ -481455,6 +442494,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -481507,10 +442550,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -481551,10 +442590,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -481597,6 +442632,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -481649,10 +442688,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -481693,10 +442728,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -481739,6 +442770,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -481791,10 +442826,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -481835,10 +442866,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -481881,6 +442908,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -481933,10 +442964,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -481969,12 +442996,12 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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"2.0.3.0+galaxy0",
- "1.6.10.43+galaxy3",
+ "1.6.17.0+galaxy3",
"1.6.3.4+galaxy1",
- "1.6.3.4",
- "1.6.17.0+galaxy3"
+ "1.6.10.43+galaxy3",
+ "1.6.10.43+galaxy1",
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]
},
{
@@ -481989,10 +443016,6 @@
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- {
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -482155,7 +443178,7 @@
],
"license": "CC-BY-4.0",
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF4_Quantitation_Workflow",
"outputs": [],
"parent_id": "microbiome/clinical-mp-4-quantitation",
@@ -482252,21 +443275,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n owner: crs4\n revisions: 1334cb4c6b68\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n owner: iuc\n revisions: 0f1724dd59d2\n tool_panel_section_label: Join, Subtract and Group\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n revisions: dbf9c561ef29\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n owner: iuc\n revisions: 328c607150ff\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: 5e33b465d8d5\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n owner: iuc\n revisions: 93d623d9979c\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "deeptivarshney",
- "bebatut",
- "bgruening",
- "beatrizserrano",
- "willemdek11",
- "gallardoalba",
- "natefoo"
- ]
- },
"contributors": [
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@@ -482280,154 +443288,6 @@
"orcid": "0000-0002-5752-2155",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
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- "gallantries",
- "erasmusmc"
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- "linkedin": "shiltemann",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
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- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
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],
"dir": "topics/microbiome/tutorials/nanopore-16S-metagenomics",
@@ -482438,13 +443298,13 @@
"topic_4038"
],
"edam_operation": [
- "Visualisation",
- "Sequence composition calculation",
- "Statistical calculation",
"Sequencing quality control",
- "Taxonomic classification",
+ "Sequence composition calculation",
"Validation",
- "Sequence contamination filtering"
+ "Taxonomic classification",
+ "Sequence contamination filtering",
+ "Visualisation",
+ "Statistical calculation"
],
"edam_topic": [
"Microbial ecology",
@@ -482483,7 +443343,7 @@
"Analyze and preprocess Nanopore reads",
"Use Kraken2 to assign a taxonomic labels"
],
- "pageviews": 4894,
+ "pageviews": 5025,
"pub_date": "2020-11-24",
"questions": [
"How can we analyse the health status of the soil?",
@@ -482497,15 +443357,15 @@
],
"short_id": "T00392",
"short_tools": [
+ "kraken2",
+ "fastp",
"fastqc",
- "datamash_reverse",
- "Remove beginning1",
"multiqc",
+ "Remove beginning1",
"tp_replace_in_line",
- "taxonomy_krona_chart",
- "fastp",
+ "datamash_reverse",
"porechop",
- "kraken2"
+ "taxonomy_krona_chart"
],
"slides": false,
"slides_recordings": false,
@@ -482573,6 +443433,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -482628,10 +443492,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -482678,11 +443538,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -482727,6 +443582,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -482779,10 +443638,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -482823,10 +443678,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -482869,6 +443720,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -482923,10 +443778,6 @@
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{
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"state": "inexact",
@@ -482973,11 +443824,6 @@
"state": "exact",
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{
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"state": "exact",
@@ -483023,6 +443869,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -483085,10 +443935,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -483139,11 +443985,6 @@
"state": "exact",
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{
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"state": "exact",
@@ -483189,6 +444030,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -483246,10 +444091,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "inexact",
@@ -483300,9 +444141,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -483313,11 +444154,6 @@
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},
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- "version": "0.72+galaxy1"
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{
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"state": "exact",
@@ -483363,6 +444199,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -483422,10 +444262,6 @@
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{
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@@ -483457,183 +444293,169 @@
{
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{
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+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
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+ ]
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+ {
+ "server": "https://usegalaxy.eu",
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},
@@ -483685,6 +444507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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"state": "missing"
@@ -483709,9 +444535,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
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"2.1.1+galaxy0",
- "2.1.1+galaxy1",
- "2.1.3+galaxy1"
+ "2.1.1+galaxy1"
]
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@@ -483848,6 +444662,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -483873,9 +444691,9 @@
"state": "inexact",
"versions": [
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+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
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{
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{
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@@ -484018,6 +444827,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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{
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@@ -484194,8 +444999,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 163,
- "visitors": 3520,
+ "visit_duration": 160,
+ "visitors": 3619,
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"creators": [],
@@ -484246,7 +445051,7 @@
],
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
"outputs": [],
"parent_id": "microbiome/nanopore-16S-metagenomics",
@@ -484433,12 +445238,12 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
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],
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- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
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"What is the importance of making a new database for quantification"
@@ -484470,17 +445275,17 @@
],
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- "dbbuilder",
- "tp_cat",
- "Remove beginning1",
- "collapse_dataset",
- "Filter1",
"pepquery2",
+ "Filter1",
+ "Cut1",
+ "dbbuilder",
"query_tabular",
+ "collapse_dataset",
+ "fasta_merge_files_and_filter_unique_sequences",
"Grouping1",
- "Cut1",
- "uniprotxml_downloader"
+ "tp_cat",
+ "uniprotxml_downloader",
+ "Remove beginning1"
],
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@@ -484533,6 +445338,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -484588,10 +445397,6 @@
"name": "InteractoMIX",
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},
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -484638,11 +445443,6 @@
"url": "https://usegalaxy.eu",
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- "usegalaxy": false
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"url": "https://usegalaxy.no/",
@@ -484687,6 +445487,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
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{
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@@ -484829,6 +445625,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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@@ -484971,6 +445763,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "local"
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{
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{
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@@ -485113,6 +445901,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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"state": "local"
@@ -485255,6 +446039,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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@@ -485309,10 +446097,6 @@
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{
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@@ -485562,6 +446336,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
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"state": "exact",
@@ -485713,6 +446482,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
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@@ -486010,6 +446771,10 @@
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},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -486117,11 +446878,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -486167,6 +446923,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -486221,10 +446981,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -486272,11 +447028,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -486471,7 +447222,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Human UniProt+Isoforms FASTA\"];\n 4bdae9fb-eb48-4821-a806-e7dd3a8c7101[\"Output\\nHuman UniProt+Isoforms FASTA\"];\n 0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;\n style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;\n 1[\"cRAP\"];\n 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa[\"Output\\ncRAP\"];\n 1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;\n style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"Human UniProt+Isoforms+cRAP FASTA\"];\n 0 -->|output_database| 6;\n 1 -->|output_database| 6;\n 62c376eb-85a3-4976-8024-bd72ac528af3[\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"];\n 6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;\n style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;\n 7[\"Cut\"];\n 3 -->|output| 7;\n 8[\"Cut\"];\n 5 -->|output| 8;\n 9[\"PepQuery2\"];\n 6 -->|output| 9;\n 4 -->|output| 9;\n 2 -->|output| 9;\n 10[\"Remove beginning\"];\n 7 -->|out_file1| 10;\n 11[\"Remove beginning\"];\n 8 -->|out_file1| 11;\n 12[\"Collapse Collection\"];\n 9 -->|psm_rank_txt| 12;\n 13[\"Concatenate datasets\"];\n 10 -->|out_file1| 13;\n 11 -->|out_file1| 13;\n 14[\"Filter\"];\n 12 -->|output| 14;\n 15[\"Remove beginning\"];\n 14 -->|out_file1| 15;\n 16[\"Cut\"];\n 15 -->|out_file1| 16;\n 17[\"Peptide and Protein from Peptide reports\"];\n 16 -->|out_file1| 17;\n 13 -->|out_file1| 17;\n bc4e33da-4064-4b78-bb15-5732b08b9316[\"Output\\nPeptide and Protein from Peptide reports\"];\n 17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;\n style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;\n 18[\"Remove beginning\"];\n 17 -->|output| 18;\n 19[\"Group\"];\n 18 -->|out_file1| 19;\n 20[\"Uniprot-ID from verified Peptides\"];\n 19 -->|out_file1| 20;\n cd6c81d8-1f44-4129-b505-2ee4dde10cd2[\"Output\\nUniprot-ID from verified Peptides\"];\n 20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;\n style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;\n 21[\"UniProt\"];\n 20 -->|output| 21;\n 22[\"Quantitation Database for MaxQuant\"];\n 0 -->|output_database| 22;\n 1 -->|output_database| 22;\n 21 -->|proteome| 22;\n a52b5136-db74-496f-9b66-ec1064f2301d[\"Output\\nQuantitation Database for MaxQuant\"];\n 22 --> a52b5136-db74-496f-9b66-ec1064f2301d;\n style a52b5136-db74-496f-9b66-ec1064f2301d stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF3_VERIFICATION_WORKFLOW",
"outputs": [
{
@@ -487124,13 +447875,13 @@
"topic_0080"
],
"edam_operation": [
- "Visualisation",
- "Sequence composition calculation",
- "Aggregation",
- "Statistical calculation",
"Sequencing quality control",
+ "Sequence composition calculation",
+ "Visualisation",
"Taxonomic classification",
- "Sequence contamination filtering"
+ "Sequence contamination filtering",
+ "Aggregation",
+ "Statistical calculation"
],
"edam_topic": [
"Metagenomics",
@@ -487171,7 +447922,7 @@
"Identify yeast species contained in a sequenced beer sample using DNA",
"Visualize the microbiome community of a beer sample"
],
- "pageviews": 2240,
+ "pageviews": 2268,
"pub_date": "2022-09-29",
"questions": [
"How can yeast strains in a beer sample be identified?",
@@ -487199,13 +447950,13 @@
],
"short_id": "T00384",
"short_tools": [
- "fastqc",
+ "kraken2",
"Filter1",
- "taxonomy_krona_chart",
"fastp",
+ "krakentools_kreport2krona",
+ "fastqc",
"porechop",
- "kraken2",
- "krakentools_kreport2krona"
+ "taxonomy_krona_chart"
],
"slides": false,
"slides_recordings": false,
@@ -487263,6 +448014,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -487318,10 +448073,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -487368,11 +448119,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -487417,6 +448163,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -487469,10 +448219,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -487513,10 +448259,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -487559,6 +448301,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -487614,10 +448360,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -487667,11 +448409,6 @@
"state": "exact",
"version": "2.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -487719,6 +448456,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -487776,10 +448517,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -487805,8 +448542,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -487830,12 +448567,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -487845,9 +448582,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -487858,11 +448595,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -487908,6 +448640,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -487963,10 +448699,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -488004,11 +448736,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -488021,11 +448753,6 @@
"state": "exact",
"version": "0.23.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -488072,6 +448799,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -488126,10 +448857,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -488163,8 +448890,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -488177,11 +448904,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -488227,6 +448949,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -488286,10 +449012,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -488334,14 +449056,6 @@
"state": "exact",
"version": "1.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.2+galaxy1",
- "1.2+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -488386,6 +449100,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -488440,10 +449158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -488489,10 +449203,6 @@
"state": "exact",
"version": "0.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -488555,8 +449265,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 178,
- "visitors": 1457,
+ "visit_duration": 179,
+ "visitors": 1480,
"workflows": [
{
"creators": [
@@ -488583,7 +449293,7 @@
"report": null,
"subworkflows": false
},
- "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"Porechop\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"fastp\"]\n 2 -> 3 [label=\"outfile\"]\n 4[label=\"Kraken2\"]\n 3 -> 4 [label=\"out1\"]\n k187b57b4dbc64b54a23430528104253c[color=lightseagreen,label=\"Output\\nkraken_report\"]\n 4 -> k187b57b4dbc64b54a23430528104253c\n 5[label=\"Filter\"]\n 4 -> 5 [label=\"report_output\"]\n 6[label=\"Filter\"]\n 4 -> 6 [label=\"report_output\"]\n 7[label=\"Krakentools: Convert kraken report file\"]\n 4 -> 7 [label=\"report_output\"]\n k869cc8a83ca44a36ae0b6b84a219aa8c[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n 7 -> k869cc8a83ca44a36ae0b6b84a219aa8c\n 8[label=\"Krona pie chart\"]\n 7 -> 8 [label=\"output\"]\n}",
+ "graph_dot": "digraph main {\n node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n edge [fontname=\"Atkinson Hyperlegible\"];\n 0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput\"]\n 1[label=\"FastQC\"]\n 0 -> 1 [label=\"output\"]\n 2[label=\"Porechop\"]\n 0 -> 2 [label=\"output\"]\n 3[label=\"fastp\"]\n 2 -> 3 [label=\"outfile\"]\n 4[label=\"Kraken2\"]\n 3 -> 4 [label=\"out1\"]\n k2f64518371f047b3a05542ba3b69f86d[color=lightseagreen,label=\"Output\\nkraken_report\"]\n 4 -> k2f64518371f047b3a05542ba3b69f86d\n 5[label=\"Filter\"]\n 4 -> 5 [label=\"report_output\"]\n 6[label=\"Filter\"]\n 4 -> 6 [label=\"report_output\"]\n 7[label=\"Krakentools: Convert kraken report file\"]\n 4 -> 7 [label=\"report_output\"]\n k25bd379d40204894870f912b763d6031[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n 7 -> k25bd379d40204894870f912b763d6031\n 8[label=\"Krona pie chart\"]\n 7 -> 8 [label=\"output\"]\n}",
"history": [
{
"hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -488623,8 +449333,8 @@
}
],
"license": "MIT",
- "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n 2[\"Porechop\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|outfile| 3;\n 4[\"Kraken2\"];\n 3 -->|out1| 4;\n 187b57b4-dbc6-4b54-a234-30528104253c[\"Output\\nkraken_report\"];\n 4 --> 187b57b4-dbc6-4b54-a234-30528104253c;\n style 187b57b4-dbc6-4b54-a234-30528104253c stroke:#2c3143,stroke-width:4px;\n 5[\"Filter\"];\n 4 -->|report_output| 5;\n 6[\"Filter\"];\n 4 -->|report_output| 6;\n 7[\"Krakentools: Convert kraken report file\"];\n 4 -->|report_output| 7;\n 869cc8a8-3ca4-4a36-ae0b-6b84a219aa8c[\"Output\\nkrakentool_report\"];\n 7 --> 869cc8a8-3ca4-4a36-ae0b-6b84a219aa8c;\n style 869cc8a8-3ca4-4a36-ae0b-6b84a219aa8c stroke:#2c3143,stroke-width:4px;\n 8[\"Krona pie chart\"];\n 7 -->|output| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FastQC\"];\n 0 -->|output| 1;\n 2[\"Porechop\"];\n 0 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|outfile| 3;\n 4[\"Kraken2\"];\n 3 -->|out1| 4;\n 2f645183-71f0-47b3-a055-42ba3b69f86d[\"Output\\nkraken_report\"];\n 4 --> 2f645183-71f0-47b3-a055-42ba3b69f86d;\n style 2f645183-71f0-47b3-a055-42ba3b69f86d stroke:#2c3143,stroke-width:4px;\n 5[\"Filter\"];\n 4 -->|report_output| 5;\n 6[\"Filter\"];\n 4 -->|report_output| 6;\n 7[\"Krakentools: Convert kraken report file\"];\n 4 -->|report_output| 7;\n 25bd379d-4020-4894-870f-912b763d6031[\"Output\\nkrakentool_report\"];\n 7 --> 25bd379d-4020-4894-870f-912b763d6031;\n style 25bd379d-4020-4894-870f-912b763d6031 stroke:#2c3143,stroke-width:4px;\n 8[\"Krona pie chart\"];\n 7 -->|output| 8;",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Identification of the micro-organisms in a beer using Nanopore sequencing",
"outputs": [
{
@@ -488672,7 +449382,7 @@
{
"label": "kraken_report",
"output_name": "report_output",
- "uuid": "187b57b4-dbc6-4b54-a234-30528104253c"
+ "uuid": "2f645183-71f0-47b3-a055-42ba3b69f86d"
}
]
},
@@ -488717,7 +449427,7 @@
{
"label": "krakentool_report",
"output_name": "output",
- "uuid": "869cc8a8-3ca4-4a36-ae0b-6b84a219aa8c"
+ "uuid": "25bd379d-4020-4894-870f-912b763d6031"
}
]
}
@@ -488953,7 +449663,6 @@
"GalaxyTrakr",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -488979,7 +449688,7 @@
"Explain different metrics to calculate \u03b1 and \u03b2 diversity",
"Apply Krakentools to calculate \u03b1 and \u03b2 diversity and understand the output"
],
- "pageviews": 1448,
+ "pageviews": 1575,
"pub_date": "2024-08-01",
"questions": [
"How many different taxons are present in my sample? How do I additionally take their relative abundance into account?",
@@ -489003,8 +449712,8 @@
],
"short_id": "T00447",
"short_tools": [
- "krakentools_beta_diversity",
- "krakentools_alpha_diversity"
+ "krakentools_alpha_diversity",
+ "krakentools_beta_diversity"
],
"slides": false,
"slides_recordings": false,
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- "url": "https://usegalaxy.fr/",
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{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -489071,6 +449775,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -489126,10 +449834,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
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"url": "https://usegalaxy.eu",
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"video_view": 0,
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- "visitors": 1216,
+ "visit_duration": 93,
+ "visitors": 1321,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Calculating diversity from microbiome taxonomic data",
"outputs": [],
"parent_id": "microbiome/diversity",
@@ -489744,8 +450433,8 @@
],
"dir": "topics/microbiome/tutorials/clinical-mp-5-data-interpretation",
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- "Prediction and recognition",
- "Visualisation"
+ "Visualisation",
+ "Prediction and recognition"
],
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"exact_supported_servers": [
@@ -489777,14 +450466,14 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-12-09",
+ "mod_date": "2024-12-13",
"objectives": [
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"Analyze significant proteins",
"Look at the taxonomic distribution of the quantified peptides"
],
"pageviews": 0,
- "pub_date": "2024-12-09",
+ "pub_date": "2024-12-13",
"questions": [
"Why do we need to interpret the data?",
"Can we visualize the data?"
@@ -489816,8 +450505,8 @@
],
"short_id": "T00464",
"short_tools": [
- "unipept",
"Grep1",
+ "unipept",
"msstatstmt"
],
"slides": false,
@@ -489870,6 +450559,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"name": "InteractoMIX",
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- "url": "http://galaxy.ul.edu.lb/"
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"usegalaxy": true
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- "url": "https://usegalaxy.fr/",
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{
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"url": "https://usegalaxy.no/",
@@ -490024,6 +450708,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
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{
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},
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{
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"state": "local"
@@ -490166,6 +450846,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"state": "missing"
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- "state": "missing"
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{
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"state": "missing"
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},
- {
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -490312,6 +450988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
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{
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -490641,7 +451313,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF5_Data_Interpretation_Worklow",
"outputs": [],
"parent_id": "microbiome/clinical-mp-5-data-interpretation",
@@ -490757,7 +451429,7 @@
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
"mod_date": "2024-03-14",
- "pageviews": 284,
+ "pageviews": 301,
"pub_date": "2024-03-14",
"short_id": "T00427",
"short_tools": [],
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 204,
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+ "visit_duration": 198,
+ "visitors": 196
},
{
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@@ -491000,12 +451672,12 @@
"topic_0196"
],
"edam_operation": [
- "Sequence composition calculation",
- "Statistical calculation",
"Sequencing quality control",
- "Genome assembly",
+ "Sequence composition calculation",
"Validation",
- "Sequence assembly validation"
+ "Genome assembly",
+ "Sequence assembly validation",
+ "Statistical calculation"
],
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"Metagenomics",
@@ -491014,8 +451686,7 @@
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"GalaxyTrakr",
"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
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"zenodo_link_results": "https://zenodo.org/record/7845138"
@@ -491049,7 +451720,7 @@
"Binning of contigs into metagenome-assembled genomes (MAGs) using MetaBAT 2 software",
"Evaluation of MAG quality and completeness using CheckM software"
],
- "pageviews": 3321,
+ "pageviews": 3403,
"pub_date": "2023-12-05",
"questions": [
"What is metagenomic binning refers to?",
@@ -491101,11 +451772,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -491143,6 +451809,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -491198,10 +451868,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -491248,11 +451914,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -491297,6 +451958,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "missing"
@@ -491449,6 +452105,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"video_versions": 1,
"video_view": 0,
- "visit_duration": 83,
- "visitors": 2719,
+ "visit_duration": 84,
+ "visitors": 2783,
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},
{
@@ -491749,7 +452400,7 @@
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"license": "CC-BY-4.0",
"mod_date": "2024-03-14",
- "pageviews": 343,
+ "pageviews": 345,
"pub_date": "2024-02-12",
"short_id": "T00412",
"short_tools": [],
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"video_view": 0,
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+ "visit_duration": 177,
+ "visitors": 192
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{
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@@ -492067,23 +452718,6 @@
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- "hexylena",
- "bedroesb",
- "willdurand",
- "njall"
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@@ -492151,171 +452785,6 @@
"orcid": "0000-0002-9970-6657",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
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- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
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- "linkedin": "shiltemann",
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- "lat": 51.912,
- "lon": 4.462
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
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- "fediverse_flavor": "mastodon",
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- "elixir-europe"
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- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bedroesb/",
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- "joined": "2017-09",
- "name": "William Durand",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
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@@ -492326,16 +452795,16 @@
"topic_4038"
],
"edam_operation": [
- "Sequence clustering",
- "Visualisation",
"Phylogenetic analysis",
+ "Phylogenetic tree analysis",
+ "Visualisation",
+ "Sequence clustering",
+ "DNA barcoding",
"Sequencing quality control",
- "Phylogenetic tree reconstruction",
- "Phylogenetic tree generation",
"Taxonomic classification",
"Sequence read processing",
- "DNA barcoding",
- "Phylogenetic tree analysis"
+ "Phylogenetic tree reconstruction",
+ "Phylogenetic tree generation"
],
"edam_topic": [
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@@ -492353,7 +452822,6 @@
"id": "microbiome/mothur-miseq-sop",
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- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -492376,7 +452844,7 @@
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],
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+ "pageviews": 10333,
"priority": 1000,
"pub_date": "2017-02-12",
"questions": [
@@ -492390,39 +452858,39 @@
],
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- "mothur_heatmap_sim",
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- "mothur_taxonomy_to_krona",
- "mothur_make_biom",
- "mothur_cluster_split",
- "mothur_sub_sample",
- "mothur_filter_seqs",
- "mothur_screen_seqs",
+ "mothur_make_contigs",
"mothur_rarefaction_single",
"mothur_dist_shared",
+ "mothur_filter_seqs",
+ "taxonomy_krona_chart",
+ "mothur_screen_seqs",
+ "mothur_summary_single",
+ "mothur_heatmap_sim",
"mothur_classify_otu",
- "mothur_count_groups",
- "mothur_count_seqs",
"mothur_dist_seqs",
- "mothur_venn",
- "mothur_make_contigs",
+ "mothur_align_seqs",
"mothur_seq_error",
+ "mothur_summary_seqs",
+ "mothur_remove_seqs",
+ "mothur_unique_seqs",
+ "mothur_sub_sample",
+ "mothur_count_seqs",
+ "mothur_venn",
+ "mothur_cluster_split",
+ "mothur_taxonomy_to_krona",
"mothur_tree_shared",
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- "mothur_classify_seqs",
- "mothur_align_seqs",
- "mothur_summary_single",
- "mothur_make_shared",
"mothur_get_groups",
- "mothur_unique_seqs",
+ "mothur_chimera_vsearch",
+ "mothur_make_biom",
+ "mothur_classify_seqs",
"newick_display",
+ "mothur_make_shared",
"mothur_pre_cluster",
- "mothur_summary_seqs",
- "mothur_remove_groups",
- "XY_Plot_1"
+ "XY_Plot_1",
+ "mothur_count_groups",
+ "mothur_cluster",
+ "mothur_remove_groups"
],
"slides": false,
"slides_recordings": false,
@@ -492446,11 +452914,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -492490,6 +452953,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -492545,10 +453012,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -492595,11 +453058,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -492644,6 +453102,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -492703,10 +453165,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -492753,14 +453211,6 @@
"state": "exact",
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- "state": "inexact",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -492811,6 +453261,300 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
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+ {
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+ "state": "missing"
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+ "state": "missing"
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+ {
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+ "state": "missing"
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+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
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+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "1.0.2"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "exact",
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+ "version": "1.0.2"
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+ "state": "exact",
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "exact",
+ "version": "1.39.5.0"
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+ "state": "missing"
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+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.39.5.0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.39.5.0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -492833,7 +453577,8 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
+ "state": "exact",
+ "version": "1.39.5.1"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -492841,8 +453586,7 @@
},
{
"server": "https://galaxytrakr.org/",
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- "version": "1.0.2"
+ "state": "missing"
},
{
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@@ -492864,10 +453608,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -492899,47 +453639,42 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
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{
"server": "https://usegalaxy.cz/",
"state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.0.2"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
},
{
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"state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
},
{
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"state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "1.0.2"
+ "version": "1.39.5.1"
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{
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"state": "missing"
}
],
- "version": "1.0.2"
+ "version": "1.39.5.1"
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@@ -495362,6 +455727,10 @@
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{
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{
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@@ -495512,6 +455872,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -495565,10 +455929,6 @@
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{
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@@ -495612,11 +455972,6 @@
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@@ -495662,6 +456017,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -495715,10 +456074,6 @@
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@@ -495812,6 +456162,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -495865,10 +456219,6 @@
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@@ -495912,11 +456262,6 @@
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{
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"state": "exact",
@@ -495962,6 +456307,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -496017,10 +456366,6 @@
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},
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{
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@@ -496066,13 +456411,6 @@
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- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -496122,6 +456460,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -496175,10 +456517,6 @@
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},
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{
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@@ -496224,11 +456562,6 @@
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},
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- "state": "exact",
- "version": "1.39.5.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -496274,6 +456607,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -496327,10 +456664,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -496374,11 +456707,6 @@
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},
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{
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"state": "exact",
@@ -496424,6 +456752,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -496477,10 +456809,6 @@
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},
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{
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@@ -496524,11 +456852,6 @@
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},
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{
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"state": "exact",
@@ -496574,6 +456897,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -496627,10 +456954,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
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"state": "missing"
@@ -496674,11 +456997,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.39.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -496724,6 +457042,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -496777,10 +457099,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -496826,11 +457144,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.39.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -496876,6 +457189,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -496930,10 +457247,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -496977,11 +457290,6 @@
"state": "exact",
"version": "1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -497027,6 +457335,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -497080,10 +457392,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -497127,11 +457435,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.39.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -497177,6 +457480,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -497230,10 +457537,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -497277,11 +457580,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.39.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -497327,6 +457625,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -497380,10 +457682,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -497427,11 +457725,6 @@
"state": "exact",
"version": "1.39.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.39.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -497477,6 +457770,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -497532,10 +457829,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -497581,13 +457874,6 @@
"state": "exact",
"version": "1.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.6+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -497680,8 +457966,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 180,
- "visitors": 6708,
+ "visit_duration": 179,
+ "visitors": 6822,
"workflows": [
{
"creators": [],
@@ -497832,7 +458118,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput FASTQ pairs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nsilva.v4.fasta\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Count.seqs\"];\n 8 -->|groups_out| 10;\n 9 -->|out_names| 10;\n 11[\"Align.seqs\"];\n 1 -->|output| 11;\n 9 -->|out_fasta| 11;\n 12[\"Summary.seqs\"];\n 10 -->|seq_count| 12;\n 11 -->|out_align| 12;\n 13[\"Screen.seqs\"];\n 10 -->|seq_count| 13;\n 11 -->|out_align| 13;\n 14[\"Filter.seqs\"];\n 13 -->|fasta_out| 14;\n 15[\"Unique.seqs\"];\n 14 -->|filteredfasta| 15;\n 13 -->|count_out| 15;\n 16[\"Pre.cluster\"];\n 15 -->|out_fasta| 16;\n 15 -->|out_count| 16;\n 17[\"Chimera.vsearch\"];\n 16 -->|fasta_out| 17;\n 16 -->|count_out| 17;\n 18[\"Remove.seqs\"];\n 17 -->|out_accnos| 18;\n 17 -->|out_count| 18;\n 16 -->|fasta_out| 18;\n 19[\"Classify.seqs\"];\n 2 -->|output| 19;\n 18 -->|count_out| 19;\n 18 -->|fasta_out| 19;\n 3 -->|output| 19;\n 2[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.fasta\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 20[\"Remove.lineage\"];\n 18 -->|count_out| 20;\n 18 -->|fasta_out| 20;\n 19 -->|taxonomy_out| 20;\n 21[\"Get.groups\"];\n 20 -->|fasta_out| 21;\n 20 -->|count_out| 21;\n 22[\"Remove.groups\"];\n 20 -->|fasta_out| 22;\n 20 -->|count_out| 22;\n 20 -->|taxonomy_out| 22;\n 23[\"Seq.error\"];\n 4 -->|output| 23;\n 21 -->|count_out| 23;\n 21 -->|fasta_out| 23;\n 24[\"Dist.seqs\"];\n 21 -->|fasta_out| 24;\n 25[\"Cluster.split\"];\n 22 -->|fasta_out| 25;\n 22 -->|count_out| 25;\n 22 -->|taxonomy_out| 25;\n 26[\"Cluster\"];\n 21 -->|count_out| 26;\n 24 -->|out_dist| 26;\n 27[\"Make.shared\"];\n 22 -->|count_out| 27;\n 25 -->|otulist| 27;\n 28[\"Classify.otu\"];\n 22 -->|count_out| 28;\n 25 -->|otulist| 28;\n 22 -->|taxonomy_out| 28;\n 29[\"Make.shared\"];\n 21 -->|count_out| 29;\n 26 -->|otulist| 29;\n 3[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.tax\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 30[\"Summary.single\"];\n 27 -->|shared| 30;\n 31[\"Count.groups\"];\n 27 -->|shared| 31;\n 32[\"Dist.shared\"];\n 27 -->|shared| 32;\n 33[\"Rarefaction.single\"];\n 27 -->|shared| 33;\n 34[\"Sub.sample\"];\n 27 -->|shared| 34;\n 35[\"Taxonomy-to-Krona\"];\n 28 -->|taxonomies| 35;\n 36[\"Rarefaction.single\"];\n 29 -->|shared| 36;\n 37[\"Tree.shared\"];\n 32 -->|distfiles| 37;\n 38[\"Heatmap.sim\"];\n 32 -->|distfiles| 38;\n 39[\"Plotting tool\"];\n 33 -->|rarefactioncurves| 39;\n 4[\"\u2139\ufe0f Input Dataset\\nHMP_MOCK.v35.fasta\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 40[\"Venn\"];\n 34 -->|shared_out| 40;\n 41[\"Make.biom\"];\n 28 -->|taxonomies| 41;\n 5 -->|output| 41;\n 34 -->|shared_out| 41;\n 42[\"Krona pie chart\"];\n 35 -->|outputfile| 42;\n 43[\"Newick Display\"];\n 37 -->|tre| 43;\n 5[\"\u2139\ufe0f Input Dataset\\nmouse.dpw.metadata\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"Make.contigs\"];\n 0 -->|output| 6;\n 7[\"Summary.seqs\"];\n 6 -->|fasta| 7;\n 8[\"Screen.seqs\"];\n 6 -->|fasta| 8;\n 6 -->|group| 8;\n 9[\"Unique.seqs\"];\n 8 -->|fasta_out| 9;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
"outputs": [],
"parent_id": "microbiome/mothur-miseq-sop",
@@ -498091,18 +458377,6 @@
},
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"topic_4038"
],
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- "Visualisation",
"Phylogenetic analysis",
+ "Phylogenetic tree analysis",
+ "Visualisation",
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+ "DNA barcoding",
"Sequencing quality control",
- "Phylogenetic tree reconstruction",
- "Phylogenetic tree generation",
"Taxonomic classification",
"Sequence read processing",
- "DNA barcoding",
- "Phylogenetic tree analysis"
+ "Phylogenetic tree reconstruction",
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],
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -502515,6 +462560,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -502571,10 +462620,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -502624,14 +462669,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -502712,8 +462749,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 324,
- "visitors": 2575,
+ "visit_duration": 318,
+ "visitors": 2645,
"workflows": [
{
"creators": [
@@ -502808,7 +462845,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nContigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGroups\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Summary.seqs\"];\n 0 -->|output| 2;\n 3[\"Screen.seqs\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Summary.seqs\"];\n 3 -->|fasta_out| 4;\n 5[\"Unique.seqs\"];\n 3 -->|fasta_out| 5;\n 6[\"Count.seqs\"];\n 3 -->|groups_out| 6;\n 5 -->|out_names| 6;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -503253,7 +463290,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Summary.seqs\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Screen.seqs\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Filter.seqs\"];\n 3 -->|fasta_out| 4;\n 5[\"Unique.seqs\"];\n 4 -->|filteredfasta| 5;\n 3 -->|count_out| 5;\n 6[\"Pre.cluster\"];\n 5 -->|out_fasta| 6;\n 5 -->|out_count| 6;\n 7[\"Summary.seqs\"];\n 6 -->|count_out| 7;\n 6 -->|fasta_out| 7;\n a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d[\"Output\\nSummary.seqs on input dataset(s): summary\"];\n 7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;\n style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;\n 8[\"Chimera.vsearch\"];\n 6 -->|fasta_out| 8;\n 6 -->|count_out| 8;\n 9[\"Remove.seqs\"];\n 8 -->|out_accnos| 9;\n 8 -->|out_count| 9;\n 6 -->|fasta_out| 9;\n 10[\"Summary.seqs\"];\n 9 -->|count_out| 10;\n 9 -->|fasta_out| 10;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -504015,7 +464052,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Classify.seqs\"];\n 2 -->|output| 4;\n 1 -->|output| 4;\n 0 -->|output| 4;\n 3 -->|output| 4;\n 5[\"Remove.lineage\"];\n 1 -->|output| 5;\n 0 -->|output| 5;\n 4 -->|taxonomy_out| 5;\n 6[\"Summary.seqs\"];\n 5 -->|count_out| 6;\n 5 -->|fasta_out| 6;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -504343,7 +464380,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMock Count Table\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMock Sequences\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Dist.seqs\"];\n 1 -->|output| 2;\n 3[\"Cluster\"];\n 0 -->|output| 3;\n 2 -->|out_dist| 3;\n 4[\"Make.shared\"];\n 0 -->|output| 4;\n 3 -->|otulist| 4;\n 5[\"Rarefaction.single\"];\n 4 -->|shared| 5;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -504711,7 +464748,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSequences\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTaxonomy\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Remove.groups\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 2 -->|output| 3;\n 4[\"Cluster.split\"];\n 3 -->|fasta_out| 4;\n 3 -->|count_out| 4;\n 3 -->|taxonomy_out| 4;\n 5[\"Make.shared\"];\n 3 -->|count_out| 5;\n 4 -->|otulist| 5;\n 6[\"Classify.otu\"];\n 3 -->|count_out| 6;\n 4 -->|otulist| 6;\n 3 -->|taxonomy_out| 6;\n 7[\"Count.groups\"];\n 5 -->|shared| 7;\n 8[\"Sub.sample\"];\n 5 -->|shared| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -505284,7 +465321,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nShared file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Rarefaction.single\"];\n 0 -->|output| 1;\n 2[\"Summary.single\"];\n 0 -->|output| 2;\n 3[\"Plotting tool\"];\n 1 -->|rarefactioncurves| 3;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -505601,7 +465638,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nSub.sample shared\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Dist.shared\"];\n 0 -->|output| 2;\n 3[\"Collapse Collection\"];\n 1 -->|output| 3;\n 4[\"Heatmap.sim\"];\n 2 -->|distfiles| 4;\n 5[\"Tree.shared\"];\n 2 -->|distfiles| 5;\n 6[\"Venn\"];\n 3 -->|output| 6;\n 7[\"Newick Display\"];\n 5 -->|tre| 7;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
"outputs": [
{
@@ -505996,17 +466033,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n owner: bgruening\n revisions: 8e214e52e461\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n owner: bgruening\n revisions: 7255688c77f3\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n owner: bgruening\n revisions: 2a868592ebcb\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n owner: bgruening\n revisions: 67ee76f0e497\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n owner: bgruening\n revisions: b59c91adeac1\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n owner: bgruening\n revisions: e2c36f62e22f\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n owner: bgruening\n revisions: 744a777e9f90\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n owner: bgruening\n revisions: a22969b08177\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n owner: bgruening\n revisions: 7fac8e7a12d5\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n owner: bgruening\n revisions: 6fe6b0e10ed6\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n owner: bgruening\n revisions: '0046692724f9'\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n owner: bgruening\n revisions: 6cbe2f30c2d7\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n owner: bgruening\n revisions: d4c67ced6abc\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n owner: bgruening\n revisions: 9b48456a96fe\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n owner: bgruening\n revisions: f6f9b47d02b6\n tool_panel_section_label: ChemicalToolBox\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 830961c48e42\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
- "contributions": {
- "authorship": [
- "simonbray"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "simonbray",
- "bgruening"
- ]
- },
"contributors": [
{
"elixir_node": "de",
@@ -506019,111 +466045,6 @@
"name": "Simon Bray",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "simonbray",
- "joined": "2019-05",
- "name": "Simon Bray",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/computational-chemistry/tutorials/covid19-docking",
@@ -506152,7 +466073,7 @@
"Replicate the study on a (very) small scale",
"Gain familiarity with the docking and scoring techniques involved."
],
- "pageviews": 4641,
+ "pageviews": 4647,
"pub_date": "2020-03-27",
"questions": [
"How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -506171,17 +466092,17 @@
"short_id": "T00049",
"short_tools": [
"sucos_max_score",
- "rdock_rbdock",
- "rxdock_rbcavity",
+ "collapse_dataset",
"openbabel_compound_convert",
- "rxdock_rbdock",
+ "rdock_rbcavity",
"xchem_pose_scoring",
- "split_file_to_collection",
- "enumerate_charges",
"xchem_transfs_scoring",
- "rdock_rbcavity",
+ "rxdock_rbdock",
+ "split_file_to_collection",
+ "rxdock_rbcavity",
"ctb_frankenstein_ligand",
- "collapse_dataset"
+ "rdock_rbdock",
+ "enumerate_charges"
],
"slides": false,
"slides_recordings": false,
@@ -506211,6 +466132,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -506266,10 +466191,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -506316,11 +466237,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -506365,6 +466281,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -506417,10 +466337,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -506466,10 +466382,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -506519,6 +466431,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -506571,10 +466487,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -506620,10 +466532,6 @@
"state": "exact",
"version": "2013.1-0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -506669,6 +466577,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -506721,10 +466633,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -506770,10 +466678,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -506823,6 +466727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -506875,10 +466783,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -506924,10 +466828,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -506973,6 +466873,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507028,10 +466932,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507077,10 +466977,6 @@
"state": "exact",
"version": "2.4.2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -507128,6 +467024,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507181,10 +467081,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507230,10 +467126,6 @@
"state": "exact",
"version": "3.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -507279,6 +467171,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507331,10 +467227,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507380,10 +467272,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -507432,6 +467320,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507484,10 +467376,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507531,10 +467419,6 @@
"state": "exact",
"version": "0.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -507583,6 +467467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507635,10 +467523,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507681,10 +467565,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -507734,6 +467614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507786,10 +467670,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -507832,10 +467712,6 @@
"state": "exact",
"version": "0.1.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -507885,6 +467761,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -507938,10 +467818,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -507989,11 +467865,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.4.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -508039,6 +467910,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508071,8 +467946,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.4.0",
- "0.5.1"
+ "0.5.1",
+ "0.4.0"
]
},
{
@@ -508095,10 +467970,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -508149,11 +468020,6 @@
"state": "exact",
"version": "0.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.5.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -508199,6 +468065,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508251,10 +468121,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -508300,10 +468166,6 @@
"state": "exact",
"version": "0.2.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -508353,6 +468215,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508405,10 +468271,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -508454,10 +468316,6 @@
"state": "exact",
"version": "2020.03.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -508503,6 +468361,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508555,10 +468417,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -508602,10 +468460,6 @@
"state": "exact",
"version": "0.4.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -508650,6 +468504,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508706,10 +468564,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -508759,14 +468613,6 @@
"state": "exact",
"version": "4.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.1",
- "5.1.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -508812,6 +468658,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -508864,10 +468714,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -508908,10 +468754,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -508978,8 +468820,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 177,
- "visitors": 2771,
+ "visit_duration": 179,
+ "visitors": 2777,
"workflows": [
{
"creators": [],
@@ -509121,7 +468963,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Enumerate changes\"];\n 0 -->|output| 3;\n 4[\"Compound conversion\"];\n 1 -->|output| 4;\n 5[\"Create Frankenstein ligand\"];\n 2 -->|output| 5;\n 6[\"Compound conversion\"];\n 3 -->|output| 6;\n 7[\"rDock cavity definition\"];\n 4 -->|outfile| 7;\n 5 -->|outfile| 7;\n 8[\"Split file\"];\n 6 -->|outfile| 8;\n 9[\"rDock docking\"];\n 4 -->|outfile| 9;\n 8 -->|list_output_sdf| 9;\n 7 -->|activesite| 9;\n 10[\"Collapse Collection\"];\n 9 -->|output| 10;\n 11[\"XChem TransFS pose scoring\"];\n 1 -->|output| 11;\n 10 -->|output| 11;\n 12[\"Max SuCOS score\"];\n 11 -->|output| 12;\n 2 -->|output| 12;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
"outputs": [
{
@@ -509547,8 +469389,8 @@
"topic_3324"
],
"edam_operation": [
- "Sequence analysis",
- "Phylogenetic tree analysis"
+ "Phylogenetic tree analysis",
+ "Sequence analysis"
],
"edam_topic": [
"Genomics",
@@ -509578,7 +469420,7 @@
"Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
"Be able to read and interrogate a phylogeny encountered in the literature"
],
- "pageviews": 2183,
+ "pageviews": 2188,
"pub_date": "2022-03-16",
"questions": [
"What information can I get from a phylogenetic tree?",
@@ -509602,8 +469444,8 @@
],
"short_id": "T00144",
"short_tools": [
- "upload1",
"interactive_tool_rstudio",
+ "upload1",
"raxml"
],
"slides": false,
@@ -509646,6 +469488,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -509701,10 +469547,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -509751,11 +469593,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -509800,6 +469637,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -509852,10 +469693,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -509896,10 +469733,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -509942,6 +469775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -509995,10 +469832,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -510044,11 +469877,6 @@
"state": "exact",
"version": "8.2.12+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "8.2.12+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -510097,6 +469925,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -510150,10 +469982,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -510197,14 +470025,6 @@
"state": "exact",
"version": "8.2.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "8.2.12+galaxy0",
- "8.2.12+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -510253,6 +470073,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -510305,10 +470129,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -510349,10 +470169,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -510409,7 +470225,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 137,
- "visitors": 1466,
+ "visitors": 1471,
"workflows": [
{
"creators": [],
@@ -510480,7 +470296,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput alignment\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"RStudio\"];\n 2[\"Estimate phylogeny with RAxML\"];\n 0 -->|output| 2;\n 9f8ae577-c583-4a2d-b64d-14c25fb859d9[\"Output\\nBest-scoring ML Tree\"];\n 2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;\n style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;\n bdb8cf2f-b553-4a96-8b55-38b4b499ab88[\"Output\\nInfo\"];\n 2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;\n style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "Mtb phylogeny",
"outputs": [
{
@@ -510978,9 +470794,9 @@
"topic_2885"
],
"edam_operation": [
+ "Phylogenetic tree visualisation",
"Antimicrobial resistance prediction",
"Variant calling",
- "Phylogenetic tree visualisation",
"Phylogenetic tree generation"
],
"edam_topic": [
@@ -511021,7 +470837,7 @@
"Identify transmission clusters based on SNP distances",
"Study the emergence and spread of drug resistance based on transmission analysis."
],
- "pageviews": 2625,
+ "pageviews": 2633,
"pub_date": "2022-03-16",
"requirements": [
{
@@ -511041,23 +470857,23 @@
],
"short_id": "T00145",
"short_tools": [
- "Grep1",
- "tp_easyjoin_tool",
+ "tp_sed_tool",
+ "collapse_dataset",
+ "snippy",
"bcftools_consensus",
- "tb_profiler_profile",
"tp_cat",
- "__MERGE_COLLECTION__",
- "snp_dists",
+ "tp_easyjoin_tool",
+ "samtools_view",
"addName",
- "tp_replace_in_line",
- "snippy",
- "collapse_dataset",
"trimmomatic",
- "upload1",
- "tp_grep_tool",
- "tp_sed_tool",
- "samtools_view",
+ "Grep1",
+ "snp_dists",
+ "__MERGE_COLLECTION__",
"snp_sites",
+ "tp_grep_tool",
+ "upload1",
+ "tb_profiler_profile",
+ "tp_replace_in_line",
"tb_variant_filter"
],
"slides": false,
@@ -511110,6 +470926,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -511165,10 +470985,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -511215,11 +471031,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -511264,6 +471075,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -511316,10 +471131,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -511360,10 +471171,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -511406,6 +471213,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -511458,10 +471269,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -511502,10 +471309,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -511548,6 +471351,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -511602,10 +471409,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -511654,11 +471457,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -511704,6 +471502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -511758,10 +471560,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -511808,11 +471606,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -511858,6 +471651,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -511912,10 +471709,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -511962,11 +471755,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -512012,6 +471800,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512066,10 +471858,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -512116,11 +471904,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -512166,6 +471949,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512220,10 +472007,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -512270,11 +472053,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -512320,6 +472098,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512376,10 +472158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -512414,10 +472192,10 @@
"state": "inexact",
"versions": [
"1.9+galaxy2",
- "1.9+galaxy1",
- "1.10",
+ "1.9",
"1.4.0",
- "1.9"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -512430,18 +472208,13 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -512484,6 +472257,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512542,10 +472319,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -512595,27 +472368,13 @@
"state": "exact",
"version": "1.9+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.15.1+galaxy3",
- "1.10+galaxy1",
- "1.9+galaxy1",
- "1.10",
- "1.15.1+galaxy0",
- "1.15.1+galaxy2",
- "1.15.1+galaxy4",
- "1.15.1+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -512629,12 +472388,12 @@
"versions": [
"1.15.1+galaxy3",
"1.10+galaxy1",
- "1.10",
- "1.4.0",
"1.9",
- "1.15.1+galaxy0",
+ "1.4.0",
+ "1.10",
+ "1.15.1+galaxy4",
"1.15.1+galaxy2",
- "1.15.1+galaxy4"
+ "1.15.1+galaxy0"
]
},
{
@@ -512667,6 +472426,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512691,8 +472454,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -512726,10 +472489,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -512781,11 +472540,6 @@
"state": "exact",
"version": "1.13+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.13+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -512831,6 +472585,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -512864,8 +472622,8 @@
"state": "inexact",
"versions": [
"4.5.0+galaxy1",
- "4.5.0",
- "4.6.0+galaxy0"
+ "4.6.0+galaxy0",
+ "4.5.0"
]
},
{
@@ -512888,10 +472646,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -512937,13 +472691,6 @@
"state": "exact",
"version": "3.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.6.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -512959,8 +472706,8 @@
"state": "inexact",
"versions": [
"4.5.0+galaxy1",
- "4.5.0",
- "4.6.0+galaxy0"
+ "4.6.0+galaxy0",
+ "4.5.0"
]
},
{
@@ -512993,6 +472740,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513046,10 +472797,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513083,14 +472830,14 @@
"state": "inexact",
"versions": [
"4.5.0",
- "3.2+galaxy1",
- "4.4.5+galaxy0",
- "4.4.3+galaxy0",
"3.2",
- "4.3.6+galaxy2",
- "4.4.5+galaxy2",
"4.4.5+galaxy1",
- "4.3.6+galaxy1"
+ "4.3.6+galaxy1",
+ "4.4.3+galaxy0",
+ "3.2+galaxy1",
+ "4.3.6+galaxy2",
+ "4.4.5+galaxy0",
+ "4.4.5+galaxy2"
]
},
{
@@ -513103,17 +472850,12 @@
"state": "exact",
"version": "4.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "3.2+galaxy1",
- "3.2"
+ "3.2",
+ "3.2+galaxy1"
]
},
{
@@ -513156,6 +472898,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513209,10 +472955,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513256,10 +472998,6 @@
"state": "exact",
"version": "0.6.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -513309,6 +473047,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513362,10 +473104,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513411,10 +473149,6 @@
"state": "exact",
"version": "0.8.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -513460,6 +473194,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513513,10 +473251,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513560,10 +473294,6 @@
"state": "exact",
"version": "2.5.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -513609,6 +473339,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513661,10 +473395,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513711,10 +473441,6 @@
"state": "exact",
"version": "0.1.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -513760,6 +473486,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513812,10 +473542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -513864,10 +473590,6 @@
"state": "exact",
"version": "0.3.5+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -513913,6 +473635,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -513965,10 +473691,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -514014,10 +473736,6 @@
"state": "exact",
"version": "0.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -514067,6 +473785,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -514119,10 +473841,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -514155,13 +473873,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.8.14+galaxy1",
+ "2.4",
+ "2.8.3+galaxy0",
"2.8.4+galaxy1",
+ "2.1.0",
"2.6.1+galaxy0",
- "2.8.3+galaxy0",
"2.6+galaxy0",
- "2.1.0",
- "2.4"
+ "2.8.14+galaxy1"
]
},
{
@@ -514176,10 +473894,6 @@
"state": "exact",
"version": "3.0.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -514225,6 +473939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -514278,10 +473996,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -514325,10 +474039,6 @@
"state": "exact",
"version": "0.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -514374,6 +474084,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -514428,10 +474142,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -514479,11 +474189,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -514529,6 +474234,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -514583,10 +474292,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -514626,8 +474331,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.38.0",
"0.36.6",
+ "0.38.0",
"0.39+galaxy2",
"0.36.5",
"0.32.3"
@@ -514643,11 +474348,6 @@
"state": "exact",
"version": "0.38.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.38.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -514696,6 +474396,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -514748,10 +474452,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -514792,10 +474492,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -514869,8 +474565,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 179,
- "visitors": 1714,
+ "visit_duration": 178,
+ "visitors": 1722,
"workflows": [
{
"creators": [],
@@ -514966,7 +474662,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Merge collections\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Samtools view BAM > SAM\"];\n 2 -->|output| 3;\n aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"Output\\nSamtools view on input dataset(s): filtered alignments\"];\n 3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;\n 4[\"Sed MTB_anc to Chromosome\"];\n 3 -->|outputsam| 4;\n 5[\"Samtools view SAM > BAM\"];\n 4 -->|output| 5;\n 6[\"TB-profiler\"];\n 5 -->|outputsam| 6;\n 7[\"Get drug resistance profile\"];\n 6 -->|output_txt| 7;\n 8[\"Add Sample Name\"];\n 7 -->|output| 8;\n 9[\"Concatenate DR profiles in a single table\"];\n 8 -->|output| 9;\n 10[\"Cleanup the table\"];\n 9 -->|out_file1| 10;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "From BAMs to drug resistance prediction with TB-profiler",
"outputs": [
{
@@ -515601,7 +475297,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Trimmomatic\"];\n 0 -->|output| 3;\n 4[\"Trimmomatic\"];\n 1 -->|output| 4;\n 5[\"Mapping and variant calling of SINGLE END FASTQs with snippy\"];\n 3 -->|fastq_out| 5;\n 2 -->|output| 5;\n 6[\"Mapping and variant calling of PAIRED END FASTQs with snippy\"];\n 4 -->|fastq_out_paired| 6;\n 2 -->|output| 6;\n 7[\"Merge PE/SE VCFs in a single collection with all samples\"];\n 5 -->|snpvcf| 7;\n 6 -->|snpvcf| 7;\n 8[\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"];\n 5 -->|snpsbam| 8;\n 6 -->|snpsbam| 8;\n 9[\"TB Variant Filter\"];\n 7 -->|output| 9;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "From Fastqs to VCFs and BAMs",
"outputs": [
{
@@ -516081,7 +475777,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Filter TB variants\"];\n 0 -->|output| 2;\n 3[\"Generate the complete genome of each of the samples\"];\n 2 -->|output1| 3;\n 1 -->|output| 3;\n ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a[\"Output\\n#{input_file}\"];\n 3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;\n style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;\n 4[\"Concatenate genomes to build a MSA\"];\n 3 -->|output_file| 4;\n 5[\"Keep only variable positions\"];\n 4 -->|out_file1| 5;\n 6[\"Calculate SNP distances\"];\n 5 -->|output_fasta| 6;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "From VCFs to SNP distance matrix",
"outputs": [
{
@@ -516729,14 +476425,14 @@
"Multiple sequence alignment",
"Global alignment",
"Sequencing quality control",
+ "Local alignment",
+ "Sequence contamination filtering",
"Sequence alignment analysis",
- "Sequence alignment",
- "Sequence analysis",
- "Read mapping",
- "Genome indexing",
"Generation",
- "Sequence contamination filtering",
- "Local alignment"
+ "Read mapping",
+ "Sequence analysis",
+ "Sequence alignment",
+ "Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -516767,7 +476463,7 @@
"Construct a sample consensus genome from mapped reads",
"Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
],
- "pageviews": 775,
+ "pageviews": 784,
"pub_date": "2023-05-15",
"questions": [
"Which special challenges does one encounter during sequence data analysis of pox viruses?",
@@ -516786,28 +476482,28 @@
],
"short_id": "T00347",
"short_tools": [
- "datamash_ops",
- "Add_a_column1",
- "upload1",
- "fastp",
- "__APPLY_RULES__",
- "EMBOSS: maskseq51",
- "rbc_mafft",
- "mimodd_info",
- "compose_text_param",
- "param_value_from_file",
"Cut1",
- "ivar_trim",
- "__ZIP_COLLECTION__",
+ "fastp",
+ "fasta_compute_length",
"Grep1",
- "ivar_consensus",
"qualimap_bamqc",
- "fasta_regex_finder",
- "fatovcf",
+ "mimodd_info",
+ "upload1",
+ "Add_a_column1",
"bwa_mem",
+ "ivar_consensus",
+ "rbc_mafft",
+ "EMBOSS: maskseq51",
+ "ivar_trim",
+ "compose_text_param",
+ "fatovcf",
"samtools_merge",
- "fasta_compute_length",
- "samtools_view"
+ "samtools_view",
+ "datamash_ops",
+ "__ZIP_COLLECTION__",
+ "__APPLY_RULES__",
+ "fasta_regex_finder",
+ "param_value_from_file"
],
"slides": false,
"slides_recordings": false,
@@ -516850,6 +476546,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -516905,10 +476605,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -516955,11 +476651,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -517004,6 +476695,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -517056,10 +476751,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -517100,10 +476791,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -517146,6 +476833,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -517198,10 +476889,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -517242,10 +476929,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -517288,6 +476971,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -517340,10 +477027,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -517384,10 +477067,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -517430,6 +477109,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -517482,10 +477165,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -517526,10 +477205,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -517572,6 +477247,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -517624,10 +477303,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -517668,10 +477343,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -517714,6 +477385,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -517773,10 +477448,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -517824,11 +477495,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -517875,6 +477541,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -517935,10 +477605,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -517972,9 +477638,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -517988,11 +477654,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -518038,6 +477699,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518091,10 +477756,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -518139,11 +477800,6 @@
"state": "exact",
"version": "5.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -518189,6 +477845,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518242,10 +477902,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -518290,11 +477946,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -518340,6 +477991,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518392,10 +478047,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -518439,11 +478090,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -518488,6 +478134,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518547,10 +478197,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -518605,11 +478251,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -518655,6 +478296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518710,10 +478355,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -518751,11 +478392,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -518768,11 +478409,6 @@
"state": "exact",
"version": "0.23.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -518819,6 +478455,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -518874,10 +478514,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -518912,8 +478548,8 @@
"state": "inexact",
"versions": [
"1.2+galaxy0",
- "1.0.1+galaxy0",
- "1.2.2+galaxy0"
+ "1.2.2+galaxy0",
+ "1.0.1+galaxy0"
]
},
{
@@ -518926,11 +478562,6 @@
"state": "exact",
"version": "1.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -518979,6 +478610,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519011,9 +478646,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3.1+galaxy3",
"1.3.1+galaxy4",
- "1.3.1+galaxy2"
+ "1.3.1+galaxy2",
+ "1.3.1+galaxy3"
]
},
{
@@ -519036,10 +478671,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -519073,9 +478704,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.0.1+galaxy0",
"1.2+galaxy0",
- "1.2.2+galaxy0"
+ "1.2.2+galaxy0",
+ "1.0.1+galaxy0"
]
},
{
@@ -519088,18 +478719,13 @@
"state": "exact",
"version": "1.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.3.1+galaxy3",
"1.3.1+galaxy4",
"1.3.1+galaxy2",
+ "1.3.1+galaxy3",
"1.3.1+galaxy0",
"1.3.1+galaxy1",
"1.2.2+galaxy1"
@@ -519145,6 +478771,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519201,10 +478831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -519251,11 +478877,6 @@
"state": "exact",
"version": "2.2.2d+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.2d+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -519301,6 +478922,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519356,10 +478981,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -519405,11 +479026,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -519455,6 +479071,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519479,8 +479099,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -519514,10 +479134,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -519567,11 +479183,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -519617,6 +479228,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519669,10 +479284,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -519715,10 +479326,6 @@
"state": "exact",
"version": "426+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -519766,6 +479373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519818,10 +479429,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -519864,10 +479471,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -519911,6 +479514,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -519947,8 +479554,8 @@
"state": "inexact",
"versions": [
"7.221.3",
- "7.508+galaxy0",
- "7.475+galaxy0"
+ "7.475+galaxy0",
+ "7.508+galaxy0"
]
},
{
@@ -519971,10 +479578,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -520027,11 +479630,6 @@
"state": "exact",
"version": "7.520+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "7.520+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -520080,6 +479678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -520135,10 +479737,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -520182,10 +479780,6 @@
"state": "exact",
"version": "0.1.8_1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -520237,6 +479831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -520289,10 +479887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -520333,10 +479927,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -520408,8 +479998,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 173,
- "visitors": 646,
+ "visit_duration": 170,
+ "visitors": 655,
"workflows": [
{
"creators": [
@@ -520506,7 +480096,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Select pool1 primers\"];\n 0 -->|output| 2;\n 3[\"Select pool2 primers\"];\n 0 -->|output| 3;\n 4[\"Compute sequence length\"];\n 1 -->|output| 4;\n 5[\"Datamash\"];\n 2 -->|out_file1| 5;\n 6[\"Datamash\"];\n 3 -->|out_file1| 6;\n 7[\"Cut\"];\n 4 -->|output| 7;\n 8[\"Compute\"];\n 5 -->|out_file| 8;\n 9[\"Get start position of Pool2\"];\n 6 -->|out_file| 9;\n 10[\"Get end position of sequence\"];\n 7 -->|out_file1| 10;\n 11[\"Get end position of Pool1\"];\n 8 -->|out_file1| 11;\n 12[\"Compose text parameter value\"];\n 9 -->|text_param| 12;\n 13[\"Compose text parameter value\"];\n 11 -->|text_param| 13;\n 10 -->|text_param| 13;\n 14[\"Mask Reference for Pool2\"];\n 1 -->|output| 14;\n 12 -->|out1| 14;\n af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n 14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n 15[\"Mask Reference for Pool1\"];\n 1 -->|output| 15;\n 13 -->|out1| 15;\n 0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n 15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "pox-virus-tiled-amplicon-ref-masking",
"outputs": [
{
@@ -520955,15 +480545,15 @@
],
"dir": "topics/variant-analysis/tutorials/sars-cov-2",
"edam_operation": [
- "Data handling",
+ "Validation",
"Sequencing quality control",
"Formatting",
- "Sequence alignment",
- "Validation",
+ "Data handling",
"SNP detection",
- "Read mapping",
- "Generation",
"Sequence contamination filtering",
+ "Generation",
+ "Read mapping",
+ "Sequence alignment",
"Genome indexing"
],
"edam_topic": [],
@@ -520979,7 +480569,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -521001,7 +480590,7 @@
"Understand how collections enable processing of sequencing data in batches",
"Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
],
- "pageviews": 19146,
+ "pageviews": 19161,
"pub_date": "2020-06-24",
"questions": [
"How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -521024,20 +480613,20 @@
],
"short_id": "T00315",
"short_tools": [
- "picard_MarkDuplicates",
- "Grep1",
- "snpeff_sars_cov_2",
- "tp_cut_tool",
- "lofreq_viterbi",
+ "Filter1",
+ "fastp",
"lofreq_indelqual",
+ "lofreq_viterbi",
"lofreq_call",
+ "bwa_mem",
"multiqc",
- "Filter1",
- "snpSift_extractFields",
+ "Grep1",
+ "picard_MarkDuplicates",
+ "tp_cut_tool",
+ "snpeff_sars_cov_2",
"fasterq_dump",
- "fastp",
"samtools_stats",
- "bwa_mem"
+ "snpSift_extractFields"
],
"slides": false,
"slides_recordings": false,
@@ -521071,11 +480660,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -521110,6 +480694,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -521165,10 +480753,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -521215,11 +480799,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -521264,6 +480843,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -521316,10 +480899,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -521360,10 +480939,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -521406,6 +480981,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -521458,10 +481037,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -521502,10 +481077,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -521548,6 +481119,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -521602,10 +481177,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -521653,11 +481224,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -521703,6 +481269,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -521760,10 +481330,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -521811,11 +481377,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -521864,6 +481425,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -521921,10 +481486,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -521974,11 +481535,6 @@
"state": "exact",
"version": "2.18.2.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522024,6 +481580,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522084,10 +481644,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -522136,11 +481692,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522186,6 +481737,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522243,10 +481798,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -522295,11 +481846,6 @@
"state": "exact",
"version": "0.20.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522348,6 +481894,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522403,10 +481953,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -522455,11 +482001,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522505,6 +482046,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522557,10 +482102,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -522609,11 +482150,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522659,6 +482195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522711,10 +482251,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -522759,11 +482295,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522809,6 +482340,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -522834,9 +482369,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -522873,10 +482408,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -522926,11 +482457,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -522976,6 +482502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -523029,10 +482559,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -523077,11 +482603,6 @@
"state": "exact",
"version": "4.5covid19"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.5covid19"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -523127,6 +482648,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -523181,10 +482706,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -523229,11 +482750,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -523279,6 +482795,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -523334,10 +482854,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -523384,28 +482900,6 @@
"state": "exact",
"version": "2.10.7+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.1+galaxy0",
- "2.10.4",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.8+galaxy0",
- "3.0.5+galaxy0",
- "2.10.7+galaxy2",
- "3.0.3+galaxy0",
- "2.11.0+galaxy1",
- "3.1.1+galaxy1",
- "3.0.8+galaxy0",
- "3.1.0+galaxy1",
- "3.0.10+galaxy0",
- "3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -523424,24 +482918,24 @@
"versions": [
"2.10.9+galaxy0",
"3.1.1+galaxy0",
+ "2.11.0+galaxy0",
"2.10.4",
"2.10.4+galaxy1",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.4+galaxy2",
"2.10.8+galaxy0",
- "2.10.7+galaxy0",
+ "2.10.4+galaxy2",
"3.0.5+galaxy0",
+ "2.10.7+galaxy0",
"3.0.3+galaxy0",
+ "3.0.5+galaxy3",
+ "3.0.8+galaxy1",
"2.11.0+galaxy1",
"3.1.1+galaxy1",
"3.0.8+galaxy0",
"3.1.0+galaxy1",
- "3.0.10+galaxy0",
"3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0",
- "3.0.5+galaxy1"
+ "3.0.10+galaxy0",
+ "3.0.5+galaxy1",
+ "3.0.0+galaxy0"
]
},
{
@@ -523474,6 +482968,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -523529,10 +483027,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -523568,10 +483062,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.10.4",
- "2.10.4+galaxy1",
"2.10.7+galaxy1",
- "2.11.0+galaxy0"
+ "2.11.0+galaxy0",
+ "2.10.4",
+ "2.10.4+galaxy1"
]
},
{
@@ -523584,11 +483078,6 @@
"state": "exact",
"version": "3.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -523660,7 +483149,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 175,
- "visitors": 12595,
+ "visitors": 12606,
"workflows": [
{
"creators": [],
@@ -523791,7 +483280,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Faster Download and Extract Reads in FASTQ\"];\n 1 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|list_paired| 3;\n 4[\"Map with BWA-MEM\"];\n 3 -->|output_paired_coll| 4;\n 0 -->|output| 4;\n 5[\"MarkDuplicates\"];\n 4 -->|bam_output| 5;\n 6[\"Realign reads\"];\n 5 -->|outFile| 6;\n 0 -->|output| 6;\n 7[\"Samtools stats\"];\n 5 -->|outFile| 7;\n 8[\"Insert indel qualities\"];\n 6 -->|realigned| 8;\n 0 -->|output| 8;\n 2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n 8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n 9[\"Call variants\"];\n 8 -->|output| 9;\n 0 -->|output| 9;\n 10[\"SnpEff eff:\"];\n 9 -->|variants| 10;\n 11[\"SnpSift Extract Fields\"];\n 10 -->|snpeff_output| 11;\n 06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n 11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n 12[\"MultiQC\"];\n 3 -->|report_json| 12;\n 7 -->|output| 12;\n 5 -->|metrics_file| 12;\n 10 -->|csvFile| 12;\n 758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n 12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Simple COVID-19 - PE Variation",
"outputs": [
{
@@ -524550,8 +484039,8 @@
"edam_operation": [
"Methylation analysis",
"Variant classification",
- "Tree-based sequence alignment",
- "Variant calling"
+ "Variant calling",
+ "Tree-based sequence alignment"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -524586,7 +484075,7 @@
"Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
"Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
],
- "pageviews": 12244,
+ "pageviews": 12257,
"pub_date": "2021-06-30",
"questions": [
"How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -524649,12 +484138,12 @@
],
"short_id": "T00316",
"short_tools": [
+ "Filter1",
"datamash_ops",
- "pangolin",
"nextclade",
"fasta_regex_finder",
- "Filter1",
- "upload1"
+ "upload1",
+ "pangolin"
],
"slides": false,
"slides_recordings": false,
@@ -524702,6 +484191,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -524757,10 +484250,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -524807,11 +484296,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -524856,6 +484340,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -524908,10 +484396,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -524952,10 +484436,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -524998,6 +484478,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -525058,10 +484542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -525109,11 +484589,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -525164,6 +484639,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -525217,10 +484696,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -525264,11 +484739,6 @@
"state": "exact",
"version": "2.7.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -525313,6 +484783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -525345,11 +484819,11 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
"3.0.3+galaxy0",
+ "4.1.1+galaxy0",
"4.0.5+galaxy0",
- "4.1.1+galaxy0"
+ "3.1.16+galaxy0",
+ "4.1.2+galaxy0"
]
},
{
@@ -525372,10 +484846,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -525425,11 +484895,6 @@
"state": "exact",
"version": "4.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -525474,6 +484939,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -525526,10 +484995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -525572,10 +485037,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -525619,6 +485080,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -525671,10 +485136,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -525715,10 +485176,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -525775,8 +485232,8 @@
"video": true,
"video_versions": 3,
"video_view": 0,
- "visit_duration": 208,
- "visitors": 6643
+ "visit_duration": 209,
+ "visitors": 6653
},
{
"admin_install": {
@@ -525928,25 +485385,6 @@
},
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -527288,7 +486355,8 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "exact",
+ "version": "5.0.0"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -527311,7 +486379,148 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "5.0.0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "5.0.0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -527354,10 +486563,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -527400,6 +486605,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -527457,10 +486666,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -527486,8 +486691,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -527511,12 +486716,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -527526,9 +486731,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -527539,11 +486744,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -527589,6 +486789,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -527614,8 +486818,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -527652,10 +486856,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -527679,8 +486879,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -527700,12 +486900,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -527718,11 +486918,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -527771,6 +486966,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -527831,10 +487030,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -527870,8 +487065,8 @@
"versions": [
"2.0.2+galaxy2",
"2.0",
- "2.0.1",
"2.0.2",
+ "2.0.1",
"2.0.2+galaxy1"
]
},
@@ -527887,11 +487082,6 @@
"state": "exact",
"version": "2.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -527941,6 +487131,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -527997,10 +487191,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -528035,10 +487225,10 @@
"state": "inexact",
"versions": [
"1.9+galaxy2",
- "1.9+galaxy1",
- "1.10",
+ "1.9",
"1.4.0",
- "1.9"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -528051,18 +487241,13 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -528105,6 +487290,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528169,10 +487358,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -528208,11 +487393,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -528227,11 +487412,6 @@
"state": "exact",
"version": "0.23.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -528248,9 +487428,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -528291,6 +487471,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528346,10 +487530,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -528385,23 +487565,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -528414,11 +487594,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -528464,6 +487639,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528516,10 +487695,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -528562,10 +487737,6 @@
"state": "exact",
"version": "20201223+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -528609,6 +487780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528663,10 +487838,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -528700,8 +487871,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -528714,11 +487885,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -528764,6 +487930,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528819,10 +487989,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -528868,10 +488034,6 @@
"state": "exact",
"version": "0.3.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -528916,6 +488078,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -528970,10 +488136,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -529022,11 +488184,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -529037,8 +488194,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -529081,6 +488238,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529139,10 +488300,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -529189,14 +488346,6 @@
"state": "exact",
"version": "2.2.2c+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.3+galaxy0",
- "2.2.2d+galaxy3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -529252,6 +488401,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529305,10 +488458,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -529342,14 +488491,14 @@
"state": "inexact",
"versions": [
"4.5.0",
- "3.2+galaxy1",
- "4.4.5+galaxy0",
- "4.4.3+galaxy0",
"3.2",
- "4.3.6+galaxy2",
- "4.4.5+galaxy2",
"4.4.5+galaxy1",
- "4.3.6+galaxy1"
+ "4.3.6+galaxy1",
+ "4.4.3+galaxy0",
+ "3.2+galaxy1",
+ "4.3.6+galaxy2",
+ "4.4.5+galaxy0",
+ "4.4.5+galaxy2"
]
},
{
@@ -529362,17 +488511,12 @@
"state": "exact",
"version": "4.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "3.2+galaxy1",
- "3.2"
+ "3.2",
+ "3.2+galaxy1"
]
},
{
@@ -529415,6 +488559,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529467,10 +488615,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -529516,10 +488660,6 @@
"state": "exact",
"version": "0.4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -529569,6 +488709,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529621,10 +488765,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -529657,13 +488797,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.8.14+galaxy1",
+ "2.4",
+ "2.8.3+galaxy0",
"2.8.4+galaxy1",
+ "2.1.0",
"2.6.1+galaxy0",
- "2.8.3+galaxy0",
"2.6+galaxy0",
- "2.1.0",
- "2.4"
+ "2.8.14+galaxy1"
]
},
{
@@ -529678,22 +488818,18 @@
"state": "exact",
"version": "6.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.8.14+galaxy1",
"2.8.4+galaxy1",
- "4.1.1+galaxy0",
+ "2.8.14+galaxy1",
"3.0.6+galaxy0",
- "3.0.8+galaxy0",
- "3.0.7+galaxy1",
+ "3.0.4+galaxy1",
"3.0.7+galaxy0",
- "3.0.4+galaxy1"
+ "4.1.1+galaxy0",
+ "3.0.7+galaxy1",
+ "3.0.8+galaxy0"
]
},
{
@@ -529736,6 +488872,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529788,10 +488928,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -529839,10 +488975,6 @@
"state": "exact",
"version": "1.0.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -529892,6 +489024,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -529944,10 +489080,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -529995,10 +489127,6 @@
"state": "exact",
"version": "1.0.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -530048,6 +489176,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -530100,10 +489232,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -530144,10 +489272,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -530222,8 +489346,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 175,
- "visitors": 6039,
+ "visit_duration": 174,
+ "visitors": 6071,
"workflows": [
{
"creators": [
@@ -530482,7 +489606,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nReads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"fastp\"];\n 0 -->|output| 5;\n 6[\"seqret\"];\n 1 -->|output| 6;\n 7[\"snippy\"];\n 4 -->|output| 7;\n 2 -->|output| 7;\n 3 -->|output| 7;\n 5 -->|output_paired_coll| 7;\n 1 -->|output| 7;\n 8[\"Kraken2\"];\n 5 -->|output_paired_coll| 8;\n c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n 8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n 083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n 8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n 9[\"QualiMap BamQC\"];\n 7 -->|snpsbam| 9;\n 10[\"mosdepth\"];\n 2 -->|output| 10;\n 7 -->|snpsbam| 10;\n 11[\"TB Variant Filter\"];\n 7 -->|snpvcf| 11;\n 12[\"TB-Profiler Profile\"];\n 7 -->|snpsbam| 12;\n 335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n 12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n 13[\"TB Variant Filter\"];\n 7 -->|snpvcf| 13;\n 14[\"Flatten collection\"];\n 9 -->|raw_data| 14;\n 15[\"Text reformatting\"];\n 10 -->|output_quantized_bed| 15;\n 16[\"Text transformation\"];\n 11 -->|output1| 16;\n 007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n 16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n 17[\"MultiQC\"];\n 5 -->|report_json| 17;\n 14 -->|output| 17;\n 59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n 17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n 18[\"bcftools consensus\"];\n 13 -->|output1| 18;\n 6 -->|out_file1| 18;\n 15 -->|outfile| 18;\n c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n 18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n 19[\"TB Variant Report\"];\n 16 -->|output| 19;\n 12 -->|results_json| 19;\n 959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n 19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n 19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:20 +0000",
"name": "TB Variant Analysis v1.0",
"outputs": [
{
@@ -531434,9 +490558,9 @@
"topic_4013"
],
"edam_operation": [
+ "Read mapping",
"Genome annotation",
- "Genome visualisation",
- "Read mapping"
+ "Genome visualisation"
],
"edam_topic": [
"Whole genome sequencing",
@@ -531449,8 +490573,7 @@
],
"exact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -531493,7 +490616,7 @@
"Get information about ARGs",
"Visualize the ARGs and plasmid genes in their genomic context"
],
- "pageviews": 2196,
+ "pageviews": 2256,
"pub_date": "2024-01-23",
"questions": [
"Which resistance genes are on a bacterial genome?",
@@ -531518,11 +490641,11 @@
"short_tools": [
"staramr_search",
"Grep1",
- "bakta",
- "bowtie2",
- "jbrowse",
"tbl2gff3",
- "upload1"
+ "upload1",
+ "jbrowse",
+ "bakta",
+ "bowtie2"
],
"slides": false,
"slides_recordings": false,
@@ -531538,11 +490661,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -531580,6 +490698,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -531635,10 +490757,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -531685,11 +490803,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -531734,6 +490847,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -531786,10 +490903,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -531830,10 +490943,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -531876,6 +490985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -531900,9 +491013,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.4.2+galaxy0",
"2.3.4.2",
- "2.4.5+galaxy1",
- "2.4.2+galaxy0"
+ "2.4.5+galaxy1"
]
},
{
@@ -531914,9 +491027,9 @@
"state": "inexact",
"versions": [
"2.4.2+galaxy0",
+ "2.3.3.1",
"2.3.4.3",
"2.2.6",
- "2.3.3.1",
"2.3.4.3+galaxy0"
]
},
@@ -531940,10 +491053,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -531979,13 +491088,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.3.4.2",
"2.4.2+galaxy0",
+ "2.3.4.2",
"2.3.4.3",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2"
]
},
@@ -531999,17 +491108,12 @@
"state": "exact",
"version": "2.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.4.5+galaxy1",
"2.4.2+galaxy0",
+ "2.4.5+galaxy1",
"2.3.4.3+galaxy0",
"2.5.3+galaxy1",
"2.2.6.2",
@@ -532056,6 +491160,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -532109,10 +491217,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -532155,11 +491259,6 @@
"state": "exact",
"version": "1.8.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -532209,6 +491308,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -532264,10 +491367,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -532303,23 +491402,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -532332,11 +491431,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -532382,6 +491476,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -532435,10 +491533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -532481,11 +491575,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -532530,6 +491619,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -532564,10 +491657,10 @@
"state": "inexact",
"versions": [
"0.7.2+galaxy0",
+ "0.9.1+galaxy0",
"0.5.1",
- "0.2.1",
"0.8.0+galaxy0",
- "0.9.1+galaxy0"
+ "0.2.1"
]
},
{
@@ -532590,10 +491683,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -532639,11 +491728,6 @@
"state": "exact",
"version": "0.10.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.10.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -532693,6 +491777,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -532745,10 +491833,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -532789,10 +491873,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -532853,8 +491933,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 205,
- "visitors": 1604,
+ "visit_duration": 203,
+ "visitors": 1652,
"workflows": [
{
"creators": [
@@ -532876,7 +491956,7 @@
"report": null,
"subworkflows": false
},
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@@ -532991,8 +492071,8 @@
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- "modified": "2024-12-09 08:53:34 +0000",
+ "mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"staramr\"];\n 0 -->|output| 3;\n 80c90033-b113-4ab0-aa74-bc854226af75[\"Output\\nstararm_detailed_summary\"];\n 3 --> 80c90033-b113-4ab0-aa74-bc854226af75;\n style 80c90033-b113-4ab0-aa74-bc854226af75 stroke:#2c3143,stroke-width:4px;\n 4[\"Bakta\"];\n 0 -->|output| 4;\n 136fe6f9-5bed-4cfa-a226-93d7b18553a2[\"Output\\nbakta_annotation_summary\"];\n 4 --> 136fe6f9-5bed-4cfa-a226-93d7b18553a2;\n style 136fe6f9-5bed-4cfa-a226-93d7b18553a2 stroke:#2c3143,stroke-width:4px;\n 5[\"Bowtie2\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n f33376ae-d468-46b6-8c9f-681067c2051e[\"Output\\nbowtie_mapping_stats\"];\n 5 --> f33376ae-d468-46b6-8c9f-681067c2051e;\n style f33376ae-d468-46b6-8c9f-681067c2051e stroke:#2c3143,stroke-width:4px;\n 6[\"Select\"];\n 3 -->|detailed_summary| 6;\n 7[\"Table to GFF3\"];\n 6 -->|out_file1| 7;\n 8[\"JBrowse\"];\n 4 -->|annotation_gff3| 8;\n 7 -->|output| 8;\n 5 -->|output| 8;\n 20eae676-6d39-4ec3-a83d-ab27abd3ab91[\"Output\\njbrowse_output\"];\n 8 --> 20eae676-6d39-4ec3-a83d-ab27abd3ab91;\n style 20eae676-6d39-4ec3-a83d-ab27abd3ab91 stroke:#2c3143,stroke-width:4px;",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "mrsa AMR gene detection",
"outputs": [
{
@@ -533064,7 +492144,7 @@
{
"label": "stararm_detailed_summary",
"output_name": "detailed_summary",
- "uuid": "2f01e653-531f-44fe-85a7-b699a47ab683"
+ "uuid": "80c90033-b113-4ab0-aa74-bc854226af75"
}
]
},
@@ -533138,7 +492218,7 @@
{
"label": "bakta_annotation_summary",
"output_name": "annotation_tsv",
- "uuid": "4a680ee0-78c4-4733-b9f0-cb1a0ebcb174"
+ "uuid": "136fe6f9-5bed-4cfa-a226-93d7b18553a2"
}
]
},
@@ -533195,7 +492275,7 @@
{
"label": "bowtie_mapping_stats",
"output_name": "mapping_stats",
- "uuid": "a3c861ca-77bf-4118-8f3e-c452427aac79"
+ "uuid": "f33376ae-d468-46b6-8c9f-681067c2051e"
}
]
},
@@ -533248,7 +492328,7 @@
{
"label": "jbrowse_output",
"output_name": "output",
- "uuid": "cf90b47e-652b-428e-8170-11929768a4d6"
+ "uuid": "20eae676-6d39-4ec3-a83d-ab27abd3ab91"
}
]
}
@@ -533378,18 +492458,6 @@
},
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- "wm75",
- "hexylena",
- "shiltemann",
- "nekrut"
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"contributors": [
{
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@@ -533407,141 +492475,23 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
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- "elixir-europe"
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- "fediverse": "https://fosstodon.org/@bgruening",
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- "fediverse_flavor": "mastodon",
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- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "id": "nekrut",
- "joined": "2017-09",
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}
],
"dir": "topics/variant-analysis/tutorials/aiv-analysis",
"edam_operation": [
- "Multiple sequence alignment",
- "Data handling",
"Phylogenetic analysis",
+ "Multiple sequence alignment",
+ "Data retrieval",
"Sequencing quality control",
- "Sequence alignment analysis",
- "De-novo assembly",
- "Sequence alignment",
"Sequence file editing",
- "Data retrieval",
- "Sequence analysis",
- "Read mapping",
- "Generation",
+ "Data handling",
"Sequence contamination filtering",
+ "Sequence alignment analysis",
+ "Generation",
+ "Read mapping",
+ "Sequence analysis",
+ "Sequence alignment",
+ "De-novo assembly",
"Genome indexing"
],
"edam_topic": [],
@@ -533586,7 +492536,7 @@
"Construct a sample consensus genome from mapped reads",
"Generate per-segment phylogenetic trees of AIV consensus sequences"
],
- "pageviews": 2102,
+ "pageviews": 2111,
"pub_date": "2022-11-21",
"questions": [
"With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
@@ -533595,22 +492545,22 @@
],
"short_id": "T00308",
"short_tools": [
+ "collapse_dataset",
+ "fastp",
+ "__RELABEL_FROM_FILE__",
+ "bwa_mem",
+ "samtools_view",
+ "ivar_consensus",
"Grep1",
+ "qualimap_bamqc",
"tp_find_and_replace",
+ "seqtk_subseq",
"vapor",
- "ivar_consensus",
- "Show beginning1",
- "rbc_mafft",
- "qualimap_bamqc",
- "__RELABEL_FROM_FILE__",
"iqtree",
+ "rbc_mafft",
"upload1",
- "fastp",
- "seqtk_subseq",
- "bwa_mem",
- "samtools_view",
- "bamtools_split_ref",
- "collapse_dataset"
+ "Show beginning1",
+ "bamtools_split_ref"
],
"slides": false,
"slides_recordings": false,
@@ -533658,6 +492608,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -533713,10 +492667,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -533763,11 +492713,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -533812,6 +492757,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -533864,10 +492813,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -533908,10 +492853,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -533954,6 +492895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -534006,10 +492951,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -534050,10 +492991,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -534096,6 +493033,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -534148,10 +493089,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -534192,10 +493129,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -534239,175 +493172,7 @@
"state": "missing"
},
{
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- "state": "missing"
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- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
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- "state": "missing"
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- "server": "http://www.freebioinfo.org/",
- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "1.1.4",
- "1.1.3"
- ]
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
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- "1.1.3"
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- "version": "9.3+galaxy1"
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
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- "1.1.0",
- "1.1.1"
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- "state": "exact",
- "version": "9.3+galaxy1"
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- "state": "exact",
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- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -534434,21 +493199,20 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.7.17.1"
+ "1.1.3",
+ "1.1.4"
]
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "exact",
- "version": "0.7.18"
+ "state": "missing"
},
{
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
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- "0.7.12.1",
- "0.7.17.2"
+ "1.1.3",
+ "1.1.4"
]
},
{
@@ -534471,14 +493235,10 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
- "version": "0.7.18"
+ "version": "9.3+galaxy1"
},
{
"server": "https://neo.engr.uconn.edu/",
@@ -534508,25 +493268,188 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.7.17.1",
- "0.1"
+ "1.1.3",
+ "1.1.2",
+ "1.1.1",
+ "1.0.0",
+ "1.1.0"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
+ "versions": [
+ "1.1.3",
+ "1.1.4",
+ "1.1.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.1.3",
+ "1.1.1",
+ "1.1.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "9.3+galaxy1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "inexact",
+ "versions": [
+ "0.7.17.1"
+ ]
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "exact",
+ "version": "0.7.18"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
"versions": [
"0.7.17.1",
+ "0.7.12.1",
"0.7.17.2"
]
},
{
- "server": "https://usegalaxy.eu",
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
"version": "0.7.18"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.7.17.1",
+ "0.1"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "0.7.17.1",
+ "0.7.17.2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.7.18"
},
@@ -534581,6 +493504,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -534633,10 +493560,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -534681,10 +493604,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -534728,6 +493647,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -534792,10 +493715,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -534833,11 +493752,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -534852,11 +493771,6 @@
"state": "exact",
"version": "0.23.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -534909,6 +493823,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -534968,10 +493886,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -535005,8 +493919,8 @@
"state": "inexact",
"versions": [
"1.5.5.3",
- "1.5.5",
- "1.5.5.1"
+ "1.5.5.1",
+ "1.5.5"
]
},
{
@@ -535021,10 +493935,6 @@
"state": "exact",
"version": "2.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -535075,6 +493985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535130,10 +494044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -535171,8 +494081,8 @@
"state": "inexact",
"versions": [
"1.2+galaxy0",
- "1.0.1+galaxy0",
- "1.2.2+galaxy0"
+ "1.2.2+galaxy0",
+ "1.0.1+galaxy0"
]
},
{
@@ -535187,11 +494097,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -535240,6 +494145,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535296,10 +494205,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -535346,11 +494251,6 @@
"state": "exact",
"version": "2.2.2d+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.2d+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -535396,6 +494296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535420,8 +494324,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -535455,10 +494359,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -535510,11 +494410,6 @@
"state": "exact",
"version": "1.20+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.20+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -535522,9 +494417,9 @@
"1.9+galaxy3",
"1.9+galaxy1",
"1.15.1+galaxy0",
- "1.13+galaxy2",
- "1.13+galaxy1",
"1.9+galaxy2",
+ "1.13+galaxy1",
+ "1.13+galaxy2",
"1.13"
]
},
@@ -535568,6 +494463,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535626,10 +494525,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -535681,11 +494576,6 @@
"state": "exact",
"version": "1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -535736,6 +494626,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535788,10 +494682,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -535834,10 +494724,6 @@
"state": "exact",
"version": "1.0.2+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -535881,6 +494767,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -535935,10 +494825,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -535986,11 +494872,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -536036,6 +494917,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -536072,8 +494957,8 @@
"state": "inexact",
"versions": [
"7.221.3",
- "7.508+galaxy0",
- "7.475+galaxy0"
+ "7.475+galaxy0",
+ "7.508+galaxy0"
]
},
{
@@ -536096,10 +494981,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -536154,11 +495035,6 @@
"state": "exact",
"version": "7.526+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "7.526+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -536207,6 +495083,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -536259,10 +495139,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -536303,10 +495179,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -536372,8 +495244,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 157,
- "visitors": 1437
+ "visit_duration": 156,
+ "visitors": 1445
},
{
"admin_install": {
@@ -536441,21 +495313,6 @@
},
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@@ -536627,13 +495336,13 @@
"topic_4038"
],
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- "Sequence composition calculation",
- "Statistical calculation",
"Sequencing quality control",
- "Taxonomic classification",
+ "Sequence composition calculation",
"Validation",
- "Sequence contamination filtering"
+ "Taxonomic classification",
+ "Sequence contamination filtering",
+ "Visualisation",
+ "Statistical calculation"
],
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@@ -536672,7 +495381,7 @@
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],
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"questions": [
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@@ -536686,15 +495395,15 @@
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"fastqc",
- "datamash_reverse",
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"multiqc",
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"tp_replace_in_line",
- "taxonomy_krona_chart",
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+ "datamash_reverse",
"porechop",
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"slides_recordings": false,
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://usegalaxy.no/",
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{
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"state": "local"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -537874,6 +496545,10 @@
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -537898,9 +496573,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
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"2.1.1+galaxy0",
- "2.1.1+galaxy1",
- "2.1.3+galaxy1"
+ "2.1.1+galaxy1"
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@@ -538037,6 +496700,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -538062,9 +496729,9 @@
"state": "inexact",
"versions": [
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+ "1.6",
"1.11+galaxy0",
- "1.7",
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@@ -538157,11 +496820,6 @@
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@@ -538207,6 +496865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
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@@ -538266,10 +496928,6 @@
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@@ -538315,10 +496973,6 @@
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@@ -538383,8 +497037,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 163,
- "visitors": 3520,
+ "visit_duration": 160,
+ "visitors": 3619,
"workflows": [
{
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@@ -538435,7 +497089,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
"outputs": [],
"parent_id": "microbiome/nanopore-16S-metagenomics",
@@ -538565,22 +497219,6 @@
},
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],
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"questions": [
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@@ -538868,16 +497318,16 @@
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"nanoplot",
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"flye",
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"upload1",
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"name": "Coloc-stats",
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"url": "https://usegalaxy.no/",
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+ ]
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@@ -540122,6 +498514,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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@@ -540146,9 +498542,9 @@
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+ "2022.09+galaxy2",
"0.8.1+galaxy0+galaxy0",
- "2022.09+galaxy2"
+ "0.8.1+galaxy2"
]
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+ "2022.09+galaxy2",
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]
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{
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"state": "exact",
@@ -540284,6 +498671,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -540341,10 +498732,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -540390,14 +498777,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -540443,6 +498822,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -540500,10 +498883,6 @@
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"state": "missing"
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{
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@@ -540549,11 +498928,6 @@
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- "state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -540599,6 +498973,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -540662,10 +499040,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -540714,17 +499088,6 @@
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- "1.16.10+galaxy0",
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- "1.16.5+galaxy7"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -540774,6 +499137,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -540834,10 +499201,6 @@
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{
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"state": "inexact",
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{
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"state": "exact",
@@ -540936,6 +499294,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -540995,10 +499357,6 @@
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{
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"state": "exact",
@@ -541097,6 +499450,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -541150,10 +499507,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -541197,11 +499550,6 @@
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- "version": "1.20.1"
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{
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"state": "exact",
@@ -541247,6 +499595,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -541299,10 +499651,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -541343,10 +499691,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -541412,7 +499756,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 171,
- "visitors": 6438,
+ "visitors": 6459,
"workflows": [
{
"creators": [],
@@ -541555,7 +499899,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Flye assembly\"];\n 1 -->|output| 4;\n 5[\"NanoPlot\"];\n 1 -->|output| 5;\n 6[\"Map with BWA-MEM\"];\n 0 -->|output| 6;\n 4 -->|consensus| 6;\n 7[\"Fasta Statistics\"];\n 4 -->|consensus| 7;\n 8[\"Bandage Info\"];\n 4 -->|assembly_gfa| 8;\n 9[\"Bandage Image\"];\n 4 -->|assembly_gfa| 9;\n 10[\"pilon\"];\n 6 -->|bam_output| 10;\n 4 -->|consensus| 10;\n 11[\"Fasta Statistics\"];\n 10 -->|output_fasta| 11;\n 12[\"Map with BWA-MEM\"];\n 2 -->|output| 12;\n 10 -->|output_fasta| 12;\n 13[\"Map with BWA-MEM\"];\n 3 -->|output| 13;\n 10 -->|output_fasta| 13;\n 14[\"Prokka\"];\n 10 -->|output_fasta| 14;\n 15[\"JBrowse\"];\n 10 -->|output_fasta| 15;\n 12 -->|bam_output| 15;\n 13 -->|bam_output| 15;\n 16[\"JBrowse\"];\n 10 -->|output_fasta| 16;\n 14 -->|out_gff| 16;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Chloroplast-genome-assembly-and-annotation",
"outputs": [
{
@@ -542571,18 +500915,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n owner: bgruening\n revisions: 291923e6f276\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n owner: bgruening\n revisions: 78c533842eeb\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 5ec9f6bceaee\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: ddddce450736\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: ea8146ee148f\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n owner: iuc\n revisions: 0dbb995c7d35\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n revisions: c59d48774d03\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n owner: iuc\n revisions: 01210c4e9144\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n owner: iuc\n revisions: fc8804320156\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n owner: iuc\n revisions: 29dabd8db6f2\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n owner: iuc\n revisions: be1d967337e4\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n owner: iuc\n revisions: a02b8b3f5a0c\n tool_panel_section_label: Nanopore\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n owner: iuc\n revisions: 72472698a2df\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "deeptivarshney",
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- "annasyme",
- "gallardoalba"
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- },
"contributors": [
{
"id": "annasyme",
@@ -542591,124 +500923,30 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
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- "elixir-europe"
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- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
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- "uni-freiburg"
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- "id": "hexylena",
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- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "id": "annasyme",
- "joined": "2017-09",
- "name": "Anna Syme",
- "orcid": "0000-0002-9906-0673",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
}
],
"dir": "topics/assembly/tutorials/largegenome",
"edam_operation": [
- "Visualisation",
- "Variant calling",
+ "Validation",
+ "Sequence assembly visualisation",
+ "Cross-assembly",
+ "Scaffolding",
"Sequencing quality control",
+ "Sequence composition calculation",
+ "Sequence contamination filtering",
+ "Sequence assembly",
"De-novo assembly",
- "Box-Whisker plot plotting",
- "Validation",
+ "Visualisation",
"Pairwise sequence alignment",
+ "Genome assembly",
+ "Base-calling",
"Sequence assembly validation",
"Transcriptome assembly",
- "Sequence assembly",
- "Scatter plot plotting",
"Statistical calculation",
- "Genome assembly",
- "Base-calling",
+ "Variant calling",
+ "Scatter plot plotting",
"Mapping assembly",
- "Sequence composition calculation",
- "Sequence assembly visualisation",
- "Cross-assembly",
- "Scaffolding",
- "Sequence contamination filtering"
+ "Box-Whisker plot plotting"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -542739,7 +500977,7 @@
"Polish the assembly",
"Assess the quality of the assembly"
],
- "pageviews": 5990,
+ "pageviews": 6048,
"pub_date": "2023-03-06",
"questions": [
"How can we assemble a large plant or animal genome?"
@@ -542760,21 +500998,21 @@
],
"short_id": "T00331",
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- "fastqc",
- "fasta-stats",
- "nanoplot",
- "multiqc",
- "flye",
- "racon",
- "medaka_consensus_pipeline",
+ "genomescope",
"minimap2",
+ "bandage_image",
"fastp",
- "quast",
"meryl",
+ "quast",
"barchart_gnuplot",
- "bandage_image",
- "busco",
- "genomescope"
+ "fastqc",
+ "racon",
+ "fasta-stats",
+ "medaka_consensus_pipeline",
+ "multiqc",
+ "nanoplot",
+ "flye",
+ "busco"
],
"slides": false,
"slides_recordings": false,
@@ -542821,6 +501059,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -542876,10 +501118,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -542926,11 +501164,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -542975,6 +501208,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -543027,10 +501264,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -543071,10 +501304,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -543117,6 +501346,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -543153,173 +501386,13 @@
"state": "inexact",
"versions": [
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- "2.6",
- "2.9.1+galaxy0",
- "2.8.2+galaxy0",
- "2.9+galaxy0"
- ]
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
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- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
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- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
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- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
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- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
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- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
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- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
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- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
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- "2.3.7"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2.6",
"2.9.1+galaxy0",
"2.8.2+galaxy0",
"2.9+galaxy0",
- "2.3.7",
- "2.3.5",
- "2.8.3+galaxy0"
+ "2.6",
+ "2.9.5+galaxy1"
]
},
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "2.9.3+galaxy0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9.3+galaxy0"
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- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "2.9.3+galaxy0"
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- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "2.9.3+galaxy0"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.9.3+galaxy0"
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- {
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- "state": "missing"
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- "version": "2.9.3+galaxy0"
- },
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- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- {
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
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- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.5.0+galaxy1"
- },
{
"server": "http://hyperbrowser.uio.no/hb/",
"state": "missing"
@@ -543340,10 +501413,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -543376,22 +501445,173 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.1",
- "1.3.1.1"
+ "2.6",
+ "2.3.7"
]
},
{
"server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.9.1+galaxy0",
+ "2.8.2+galaxy0",
+ "2.9+galaxy0",
+ "2.6",
+ "2.3.7",
+ "2.3.5",
+ "2.8.3+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.9.3+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2.9.3+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "2.9.3+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2.9.3+galaxy0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "2.9.3+galaxy0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
"state": "exact",
"version": "1.5.0+galaxy1"
},
{
- "server": "https://usegalaxy.eu",
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "1.3.1.1",
+ "1.3.1"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
"state": "exact",
"version": "1.5.0+galaxy1"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.5.0+galaxy1"
},
@@ -543445,6 +501665,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -543470,8 +501694,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -543508,10 +501732,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -543535,8 +501755,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -543556,12 +501776,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -543574,11 +501794,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -543627,6 +501842,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -543684,10 +501903,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -543737,11 +501952,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -543787,6 +501997,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -543819,10 +502033,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -543845,10 +502059,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -543896,23 +502106,18 @@
"state": "exact",
"version": "5.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.5.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -543955,6 +502160,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544012,10 +502221,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -544061,11 +502266,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -544111,6 +502311,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544175,10 +502379,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -544214,11 +502414,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -544233,11 +502433,6 @@
"state": "exact",
"version": "0.23.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -544254,9 +502449,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -544297,6 +502492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544350,10 +502549,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -544396,11 +502591,6 @@
"state": "exact",
"version": "2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -544446,6 +502636,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544478,9 +502672,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
+ "1.0.3+galaxy1",
"1.0.3+galaxy2",
- "1.3.2+galaxy0",
- "1.0.3+galaxy1"
+ "1.3.2+galaxy0"
]
},
{
@@ -544503,10 +502697,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -544552,11 +502742,6 @@
"state": "exact",
"version": "1.7.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7.2+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -544607,6 +502792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544639,8 +502828,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -544663,10 +502852,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -544709,11 +502894,6 @@
"state": "exact",
"version": "1.3+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy6"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -544758,6 +502938,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544782,8 +502966,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.24+galaxy0",
- "2.28+galaxy0"
+ "2.28+galaxy0",
+ "2.24+galaxy0"
]
},
{
@@ -544795,8 +502979,8 @@
"state": "inexact",
"versions": [
"2.28+galaxy0",
- "2.17+galaxy0",
- "2.17+galaxy4"
+ "2.17+galaxy4",
+ "2.17+galaxy0"
]
},
{
@@ -544819,10 +503003,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -544859,12 +503039,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -544877,11 +503057,6 @@
"state": "exact",
"version": "2.26+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.26+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -544930,6 +503105,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -544984,10 +503163,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -545036,11 +503211,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -545051,8 +503221,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -545095,6 +503265,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -545156,10 +503330,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -545213,11 +503383,6 @@
"state": "exact",
"version": "1.42.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.42.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -545267,6 +503432,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -545321,10 +503490,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -545361,8 +503526,8 @@
"5.0.2+galaxy0",
"5.0.2+galaxy1",
"4.6.3",
- "5.0.2",
- "4.1"
+ "4.1",
+ "5.0.2"
]
},
{
@@ -545375,11 +503540,6 @@
"state": "exact",
"version": "5.2.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.2.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -545450,7 +503610,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 129,
- "visitors": 4581,
+ "visitors": 4628,
"workflows": [
{
"creators": [
@@ -545625,7 +503785,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 4;\n 1 -->|output| 4;\n 2 -->|output| 4;\n 5[\"Medaka polish\"];\n 4 -->|Assembly polished by long reads using Racon| 5;\n 1 -->|output| 5;\n e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n 5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n 6[\"Fasta statistics after Racon long read polish\"];\n 4 -->|Assembly polished by long reads using Racon| 6;\n 7[\"Fasta statistics after Medaka polish\"];\n 5 -->|out_consensus| 7;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 5 -->|out_consensus| 8;\n 3 -->|output| 8;\n 9[\"Fasta statistics after Racon short read polish\"];\n 8 -->|Assembly polished by short reads using Racon| 9;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assembly polishing - upgraded",
"outputs": [
{
@@ -546463,7 +504623,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Flye: assembly\"];\n 0 -->|output| 1;\n 3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n 1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n 1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n 48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n 1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n 8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n 1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n 2[\"Fasta statistics\"];\n 1 -->|consensus| 2;\n 3[\"Quast genome report\"];\n 1 -->|consensus| 3;\n 17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s): HTML report\"];\n 3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n 4[\"Bandage image: Flye assembly\"];\n 1 -->|assembly_gfa| 4;\n e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n 4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n 5[\"Bar chart: show contig sizes\"];\n 1 -->|assembly_info| 5;\n 6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n 5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assembly with Flye - upgraded",
"outputs": [
{
@@ -546808,7 +504968,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Busco: assess assembly\"];\n 0 -->|output| 2;\n 219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n 2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n 3[\"Quast: assess assembly\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s): HTML report\"];\n 3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Assess genome quality - upgraded",
"outputs": [
{
@@ -547139,7 +505299,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n style 5 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 5;\n 6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n style 6 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 6;\n 2 -->|output| 6;\n 0 -->|output| 6;\n 7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n style 7 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 7;\n 2 -->|output| 7;\n 0 -->|output| 7;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 7 -->|fastp filtered long reads| 8;\n 9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n style 9 fill:#edd,stroke:#900,stroke-width:4px;\n 8 -->|Flye assembly on input datasets consensus| 9;\n 7 -->|fastp filtered R1 reads| 9;\n 7 -->|fastp filtered long reads| 9;\n 3 -->|output| 9;\n 10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n style 10 fill:#edd,stroke:#900,stroke-width:4px;\n 9 -->|Assembly polished by long reads using Medaka| 10;\n 4 -->|output| 10;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Combined workflows for large genome assembly - upgraded ",
"outputs": [
{
@@ -548675,7 +506835,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Nanoplot: long reads\"];\n 0 -->|output| 3;\n 73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n 3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC on R1\"];\n 1 -->|output| 4;\n 5[\"FastQC on R2\"];\n 2 -->|output| 5;\n 6[\"MultiQC: combine fastQC reports\"];\n 4 -->|text_file| 6;\n 5 -->|text_file| 6;\n 8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n 6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Data QC - upgraded",
"outputs": [
{
@@ -548948,7 +507108,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Minimap2 round 1: map reads to assembly\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Racon round 1: polish assembly\"];\n 0 -->|output| 3;\n 2 -->|alignment_output| 3;\n 1 -->|output| 3;\n 4[\"Minimap2 round 2: map reads to assembly\"];\n 1 -->|output| 4;\n 3 -->|consensus| 4;\n 5[\"Racon round 2: polish assembly\"];\n 3 -->|consensus| 5;\n 4 -->|alignment_output| 5;\n 1 -->|output| 5;\n 594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n 5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
"outputs": [
{
@@ -549183,7 +507343,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"Minimap2: map long reads to assembly\"];\n 2 -->|output| 3;\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Racon: polish 1\"];\n 0 -->|output| 4;\n 3 -->|alignment_output| 4;\n 1 -->|output| 4;\n 5[\"Minimap2: map long reads to polished assembly 1\"];\n 2 -->|output| 5;\n 1 -->|output| 5;\n 4 -->|consensus| 5;\n 6[\"Racon: polish 2\"];\n 4 -->|consensus| 6;\n 5 -->|alignment_output| 6;\n 1 -->|output| 6;\n 7[\"Minimap2: map long reads to polished assembly 2\"];\n 2 -->|output| 7;\n 1 -->|output| 7;\n 6 -->|consensus| 7;\n 8[\"Racon: polish 3\"];\n 6 -->|consensus| 8;\n 7 -->|alignment_output| 8;\n 1 -->|output| 8;\n 9[\"Minimap2: map long reads to polished assembly 3\"];\n 2 -->|output| 9;\n 1 -->|output| 9;\n 8 -->|consensus| 9;\n 10[\"Racon: polish 4\"];\n 8 -->|consensus| 10;\n 9 -->|alignment_output| 10;\n 1 -->|output| 10;\n bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n 10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Racon polish with long reads, x4 - upgraded",
"outputs": [
{
@@ -549445,7 +507605,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"fastp on short reads\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n 3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n 0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n 3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n 10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n 3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n 639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n 3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n 4[\"fastp on long reads\"];\n 2 -->|output| 4;\n 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n 4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n 4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n 69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n 4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "Trim and filter reads - fastp - upgraded ",
"outputs": [
{
@@ -549772,7 +507932,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Meryl - count kmers\"];\n 0 -->|output| 1;\n 899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n 1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n 2[\"Meryl - generate histogram\"];\n 1 -->|read_db| 2;\n 3[\"Genomescope\"];\n 2 -->|read_db_hist| 3;\n efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n 3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n 701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n 3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n 85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n 3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n 3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:15 +0000",
"name": "kmer counting - meryl - upgraded",
"outputs": [
{
@@ -550164,24 +508324,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n owner: bgruening\n revisions: 7d9ee8cd14b8\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n owner: bgruening\n revisions: '392811378515'\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n owner: bgruening\n revisions: e8ac2b53f262\n tool_panel_section_label: NCBI Blast\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n owner: bgruening\n revisions: 5799092ffdff\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n owner: bgruening\n revisions: 3ef480892a9f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n owner: devteam\n revisions: 3a0efe14891f\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n owner: galaxy-australia\n revisions: 5e0825476fb7\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n owner: iuc\n revisions: ddddce450736\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n owner: iuc\n revisions: 25ca5d73aedf\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: bb935709506a\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n owner: iuc\n revisions: 2babe6d5c561\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n owner: iuc\n revisions: b4a22d90cce9\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n owner: iuc\n revisions: 01210c4e9144\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n owner: iuc\n revisions: f8113c25bc6b\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n owner: iuc\n revisions: 29dabd8db6f2\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n owner: iuc\n revisions: 5cc34c3f440d\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n owner: iuc\n revisions: dfb8a4497339\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n owner: iuc\n revisions: c6cec5ab35c1\n tool_panel_section_label: Assembly\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n owner: iuc\n revisions: 44c66e8d21e6\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n owner: nml\n revisions: 90981f86000f\n tool_panel_section_label: Collection Operations\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
- "contributions": {
- "authorship": [
- "GitFab93",
- "gallardoalba",
- "tbrown91",
- "delphine-l"
- ],
- "reviewing": [
- "teresa-m",
- "delphine-l",
- "bgruening",
- "tbrown91",
- "SaimMomin12",
- "shiltemann",
- "deeptivarshney",
- "gallardoalba"
- ]
- },
"contributors": [
{
"id": "GitFab93",
@@ -550220,158 +508362,24 @@
"orcid": "0000-0001-6421-3484",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
- {
- "email": "delphine.lariviere@galaxy.org",
- "id": "delphine-l",
- "joined": "2017-09",
- "name": "Delphine Lariviere",
- "orcid": "0000-0001-6421-3484",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "brown@izw-berlin.de",
- "id": "tbrown91",
- "joined": "2024-08",
- "name": "Tom Brown",
- "orcid": "0000-0001-8293-4816",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "email": "momins@informatik.uni-freiburg.de",
- "id": "SaimMomin12",
- "joined": "2024-03",
- "linkedin": "saim-momin",
- "matrix": "saimmomin:matrix.org",
- "name": "Saim Momin",
- "orcid": "0009-0003-9935-828X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/SaimMomin12/",
- "twitter": "SaimMomin12",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/SaimMomin12.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "deeptivarshney",
- "joined": "2022-12",
- "name": "Deepti Varshney",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
}
],
"dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
"edam_operation": [
- "Data handling",
+ "Pairwise sequence alignment",
"Genome assembly",
- "Genotyping",
+ "Sequence assembly validation",
+ "Sequence assembly visualisation",
+ "Transcriptome assembly",
+ "Scaffolding",
+ "Phasing",
+ "Data handling",
"Sequence alignment analysis",
- "Pairwise sequence alignment",
+ "k-mer counting",
"Sequence alignment",
"De-novo assembly",
"Sequence trimming",
- "Sequence assembly validation",
- "k-mer counting",
- "Phasing",
- "Sequence assembly visualisation",
- "Transcriptome assembly",
- "Scaffolding"
+ "Genotyping"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -550400,7 +508408,7 @@
"Apply the post-assembly-QC-workflow using the necessary tools",
"Analyse and evaluate the results of the workflow"
],
- "pageviews": 1465,
+ "pageviews": 1496,
"pub_date": "2023-06-23",
"questions": [
"What combination of tools can assess the quality of a genome assembly?",
@@ -550424,26 +508432,26 @@
],
"short_id": "T00355",
"short_tools": [
- "gfastats",
- "minimap2",
- "bellerophon",
- "CONVERTER_gz_to_uncompressed",
+ "genomescope",
"meryl",
- "busco",
+ "CONVERTER_gz_to_uncompressed",
+ "pretext_map",
+ "__EXTRACT_DATASET__",
"smudgeplot",
- "bg_diamond",
- "bandage_image",
- "genomescope",
- "collapse_dataset",
"bwa_mem2",
- "interactive_tool_blobtoolkit",
+ "busco",
"blobtoolkit",
- "tp_find_and_replace",
- "pretext_map",
+ "bandage_image",
+ "minimap2",
"merqury",
- "__EXTRACT_DATASET__",
- "samtools_stats",
- "pretext_snapshot"
+ "bellerophon",
+ "gfastats",
+ "interactive_tool_blobtoolkit",
+ "collapse_dataset",
+ "bg_diamond",
+ "tp_find_and_replace",
+ "pretext_snapshot",
+ "samtools_stats"
],
"slides": false,
"slides_recordings": false,
@@ -550490,6 +508498,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -550545,10 +508557,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -550595,11 +508603,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -550644,6 +508647,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -550696,10 +508703,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -550740,10 +508743,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -550786,6 +508785,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -550838,10 +508841,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -550882,10 +508881,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -550928,6 +508923,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -550980,10 +508979,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551024,10 +509019,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -551070,6 +509061,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551122,10 +509117,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551171,10 +509162,6 @@
"state": "exact",
"version": "3.4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -551225,6 +509212,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551277,10 +509268,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551326,10 +509313,6 @@
"state": "exact",
"version": "4.0.7+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -551374,6 +509357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551433,10 +509420,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551479,11 +509462,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -551529,6 +509507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551585,10 +509567,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551631,10 +509609,6 @@
"state": "exact",
"version": "1.2.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -551649,9 +509623,9 @@
"state": "inexact",
"versions": [
"1.3.6+galaxy0",
+ "1.3.5+galaxy2",
"1.3.5+galaxy0",
"1.3.4+galaxy0",
- "1.3.5+galaxy2",
"1.3.8+galaxy0",
"1.3.9+galaxy0"
]
@@ -551686,6 +509660,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551739,10 +509717,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -551785,10 +509759,6 @@
"state": "exact",
"version": "1.3.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -551833,6 +509803,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -551887,10 +509861,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -551927,10 +509897,10 @@
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
"1.1.2",
+ "1.1.1",
"1.0.0",
- "1.1.1"
+ "1.1.0"
]
},
{
@@ -551943,18 +509913,13 @@
"state": "exact",
"version": "1.1.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.3",
- "1.1.0",
- "1.1.1"
+ "1.1.1",
+ "1.1.0"
]
},
{
@@ -551997,6 +509962,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552052,10 +510021,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -552093,8 +510058,8 @@
"versions": [
"2.0.2+galaxy2",
"2.0",
- "2.0.1",
"2.0.2",
+ "2.0.1",
"2.0.2+galaxy1"
]
},
@@ -552108,11 +510073,6 @@
"state": "exact",
"version": "2.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -552158,6 +510118,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552210,10 +510174,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -552258,10 +510218,6 @@
"state": "exact",
"version": "0.2.5+galaxy+2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -552312,6 +510268,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552369,10 +510329,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -552422,11 +510378,6 @@
"state": "exact",
"version": "2022.09+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2022.09+galaxy4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -552472,6 +510423,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552524,10 +510479,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -552570,10 +510521,6 @@
"state": "exact",
"version": "1.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -552618,6 +510565,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552671,10 +510622,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -552722,41 +510669,36 @@
"state": "exact",
"version": "5.4.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.4.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "5.4.6+galaxy0",
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
+ "5.4.6+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "3.0.2+galaxy2",
- "4.1.2",
"5.3.2+galaxy0",
"5.5.0+galaxy0",
- "5.2.2+galaxy0",
+ "3.0.2+galaxy2",
+ "5.8.0+galaxy0",
"5.7.1+galaxy0",
- "5.8.0+galaxy0"
+ "4.1.2",
+ "5.2.2+galaxy0"
]
},
{
@@ -552794,6 +510736,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -552826,10 +510772,10 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "5.4.4+galaxy0",
- "5.4.6+galaxy0",
+ "5.2.2+galaxy2",
"5.0.0+galaxy0",
- "5.2.2+galaxy2"
+ "5.4.6+galaxy0",
+ "5.4.4+galaxy0"
]
},
{
@@ -552852,10 +510798,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -552903,23 +510845,18 @@
"state": "exact",
"version": "5.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.7.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "5.0.0+galaxy0",
"5.2.2+galaxy2",
+ "5.0.0+galaxy0",
"4.1.4",
"5.3.1+galaxy0",
- "4.1.2",
"5.3.2+galaxy0",
- "5.2.2+galaxy0",
- "5.2.1+galaxy0"
+ "4.1.2",
+ "5.2.1+galaxy0",
+ "5.2.2+galaxy0"
]
},
{
@@ -552962,6 +510899,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553015,10 +510956,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -553062,13 +510999,6 @@
"state": "exact",
"version": "2.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.2.1+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -553113,6 +511043,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553166,10 +511100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -553212,11 +511142,6 @@
"state": "exact",
"version": "2.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -553262,6 +511187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553314,10 +511243,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -553360,11 +511285,6 @@
"state": "exact",
"version": "1.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -553409,6 +511329,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553441,8 +511365,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3+galaxy1",
- "1.2+galaxy1"
+ "1.2+galaxy1",
+ "1.3+galaxy1"
]
},
{
@@ -553465,10 +511389,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -553511,11 +511431,6 @@
"state": "exact",
"version": "1.3+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3+galaxy6"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -553560,6 +511475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553614,10 +511533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -553654,12 +511569,12 @@
"state": "inexact",
"versions": [
"2.17+galaxy0",
- "2.5+gx1",
+ "2.17+galaxy1",
"2.3",
- "2.17",
+ "2.5+gx1",
"2.12",
- "2.5",
- "2.17+galaxy1"
+ "2.17",
+ "2.5"
]
},
{
@@ -553674,11 +511589,6 @@
"state": "exact",
"version": "2.28+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.28+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -553727,6 +511637,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553779,10 +511693,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -553825,10 +511735,6 @@
"state": "exact",
"version": "0.1.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -553873,6 +511779,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -553925,10 +511835,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -553973,10 +511879,6 @@
"state": "exact",
"version": "0.1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -554021,6 +511923,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -554073,10 +511979,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -554119,10 +512021,6 @@
"state": "exact",
"version": "0.0.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -554167,6 +512065,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -554221,10 +512123,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -554272,11 +512170,6 @@
"state": "exact",
"version": "5.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -554356,8 +512249,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 117,
- "visitors": 1119,
+ "visit_duration": 119,
+ "visitors": 1142,
"workflows": [
{
"creators": [
@@ -554680,7 +512573,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n style 5 fill:#ded,stroke:#393,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"Meryl\"];\n 3 -->|output| 9;\n 10[\"Collapse Collection\"];\n 3 -->|output| 10;\n 11[\"Create BlobtoolKit\"];\n 4 -->|output| 11;\n 0 -->|output| 11;\n 2 -->|output| 11;\n 1 -->|output| 11;\n 12[\"gfastats\"];\n 4 -->|output| 12;\n 13[\"Convert compressed file to uncompressed.\"];\n 4 -->|output| 13;\n 14[\"gfastats\"];\n 4 -->|output| 14;\n 15[\"Diamond\"];\n 4 -->|output| 15;\n 6 -->|output| 15;\n 16[\"Collapse Collection\"];\n 7 -->|output| 16;\n 17[\"Collapse Collection\"];\n 8 -->|output| 17;\n 18[\"Meryl\"];\n 9 -->|read_db| 18;\n 19[\"Map with minimap2\"];\n 10 -->|output| 19;\n 4 -->|output| 19;\n 20[\"Smudgeplot\"];\n 10 -->|output| 20;\n 21[\"Replace\"];\n 13 -->|output1| 21;\n 22[\"Bandage Image\"];\n 14 -->|output| 22;\n 23[\"BWA-MEM2\"];\n 16 -->|output| 23;\n 4 -->|output| 23;\n 24[\"BWA-MEM2\"];\n 17 -->|output| 24;\n 4 -->|output| 24;\n 25[\"Merqury\"];\n 4 -->|output| 25;\n 18 -->|read_db| 25;\n d2dbf498-5155-43b2-bf2a-ffed5c45100d[\"Output\\nMerqury on input dataset(s): stats\"];\n 25 --> d2dbf498-5155-43b2-bf2a-ffed5c45100d;\n style d2dbf498-5155-43b2-bf2a-ffed5c45100d stroke:#2c3143,stroke-width:4px;\n 0b43d206-253f-4c0b-a1f4-971402851c6d[\"Output\\nMerqury on input dataset(s): plots\"];\n 25 --> 0b43d206-253f-4c0b-a1f4-971402851c6d;\n style 0b43d206-253f-4c0b-a1f4-971402851c6d stroke:#2c3143,stroke-width:4px;\n 811a77e8-eb99-4dc7-9295-f0000fcb9fe5[\"Output\\nMerqury on input dataset(s): QV stats\"];\n 25 --> 811a77e8-eb99-4dc7-9295-f0000fcb9fe5;\n style 811a77e8-eb99-4dc7-9295-f0000fcb9fe5 stroke:#2c3143,stroke-width:4px;\n 26[\"Meryl\"];\n 18 -->|read_db| 26;\n 27[\"Samtools stats\"];\n 19 -->|alignment_output| 27;\n 28[\"Busco\"];\n 21 -->|outfile| 28;\n af98aae6-f1a3-493c-9cef-08e0926210d3[\"Output\\nBusco on input dataset(s): full table\"];\n 28 --> af98aae6-f1a3-493c-9cef-08e0926210d3;\n style af98aae6-f1a3-493c-9cef-08e0926210d3 stroke:#2c3143,stroke-width:4px;\n 929439b7-c688-45ea-848a-97c13d3e0028[\"Output\\nBusco on input dataset(s): short summary\"];\n 28 --> 929439b7-c688-45ea-848a-97c13d3e0028;\n style 929439b7-c688-45ea-848a-97c13d3e0028 stroke:#2c3143,stroke-width:4px;\n 29[\"Filter and merge\"];\n 24 -->|bam_output| 29;\n 23 -->|bam_output| 29;\n 30[\"Merqury plot 2\"];\n 25 -->|png_files| 30;\n 31[\"Merqury plot 1\"];\n 25 -->|png_files| 31;\n 32[\"Merqury plot 3\"];\n 25 -->|png_files| 32;\n 33[\"Merqury plot 5\"];\n 25 -->|png_files| 33;\n 34[\"Merqury plot 4\"];\n 25 -->|png_files| 34;\n 35[\"GenomeScope\"];\n 26 -->|read_db_hist| 35;\n 5 -->|output| 35;\n 36[\"BlobToolKit\"];\n 15 -->|blast_tabular| 36;\n 11 -->|blobdir| 36;\n 28 -->|busco_table| 36;\n 19 -->|alignment_output| 36;\n 37[\"PretextMap\"];\n 29 -->|outfile| 37;\n 38[\"BlobToolKit\"];\n 36 -->|blobdir| 38;\n 39[\"BlobToolKit\"];\n 36 -->|blobdir| 39;\n 40[\"BlobToolKit\"];\n 36 -->|blobdir| 40;\n 41[\"Pretext Snapshot\"];\n 37 -->|pretext_map_out| 41;",
- "modified": "2024-12-09 08:53:32 +0000",
+ "modified": "2024-12-13 13:26:14 +0000",
"name": "Post-assembly workflow",
"outputs": [
{
@@ -555317,23 +513210,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n owner: bgruening\n revisions: e3d32471da11\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n owner: bgruening\n revisions: 949f01671246\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n owner: galaxyp\n revisions: 3c623e81be77\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n owner: iuc\n revisions: 6a3a025714d3\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: b2f1f75d49c4\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: 5e33b465d8d5\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sample_seqs\n owner: peterjc\n revisions: 7c40a1fbc82e\n tool_panel_section_label: Filter and Sort\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_mapper\n owner: rnateam\n revisions: a8d24f4b6d95\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_quantifier\n owner: rnateam\n revisions: d5ea61ff12eb\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: targetfinder\n owner: rnateam\n revisions: c9d56748fbde\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
- "contributions": {
- "authorship": [
- "gallardoalba",
- "pavanvidem",
- "beatrizserrano"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening",
- "bebatut",
- "beatrizserrano",
- "pavanvidem",
- "gallardoalba",
- "hexylena",
- "natefoo"
- ]
- },
"contributors": [
{
"elixir_node": "de",
@@ -555371,188 +513247,21 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
"twitter": "BSerranoSolano",
"url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "beatrizserrano.galaxy@gmail.com",
- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "pavanvidem",
- "joined": "2017-09",
- "name": "Pavankumar Videm",
- "orcid": "0000-0002-5192-126X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "email": "nate@bx.psu.edu",
- "id": "natefoo",
- "joined": "2017-12",
- "matrix": "natefoo:matrix.org",
- "name": "Nate Coraor",
- "orcid": "0000-0001-8083-2963",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
}
],
"dir": "topics/transcriptomics/tutorials/mirna-target-finder",
"edam_operation": [
- "Statistical calculation",
+ "RNA-Seq quantification",
+ "Validation",
+ "Sequence trimming",
"RNA-Seq analysis",
+ "Statistical calculation",
"Sequencing quality control",
- "Gene expression analysis",
- "Read pre-processing",
+ "Sequence composition calculation",
"Primer removal",
- "Validation",
"Differential gene expression analysis",
- "Sequence composition calculation",
- "RNA-Seq quantification",
- "Sequence trimming"
+ "Gene expression analysis",
+ "Read pre-processing"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -555584,7 +513293,7 @@
"Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
"Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
],
- "pageviews": 5673176,
+ "pageviews": 5696023,
"pub_date": "2021-04-08",
"questions": [
"Which miRNAs are upregulated in response to brassinosteroids?",
@@ -555606,20 +513315,20 @@
],
"short_id": "T00292",
"short_tools": [
+ "cat1",
+ "Filter1",
+ "Cut1",
"deseq2",
- "fastqc",
- "filter_by_fasta_ids",
+ "sample_seqs",
"rbc_mirdeep2_mapper",
"rbc_mirdeep2_quantifier",
- "__MERGE_COLLECTION__",
- "multiqc",
- "Filter1",
"sort1",
- "sample_seqs",
- "targetfinder",
+ "fastqc",
+ "multiqc",
+ "__MERGE_COLLECTION__",
"salmon",
- "cat1",
- "Cut1",
+ "targetfinder",
+ "filter_by_fasta_ids",
"trim_galore"
],
"slides": true,
@@ -555697,6 +513406,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -555752,10 +513465,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -555802,11 +513511,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -555851,6 +513555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -555903,10 +513611,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -555947,10 +513651,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -555993,6 +513693,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -556045,10 +513749,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -556089,10 +513789,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -556135,6 +513831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -556187,10 +513887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -556231,10 +513927,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -556277,6 +513969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -556329,10 +514025,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -556373,10 +514065,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -556419,6 +514107,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -556471,10 +514163,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -556515,10 +514203,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -556561,6 +514245,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -556616,10 +514304,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -556656,13 +514340,13 @@
"state": "inexact",
"versions": [
"1.10.1+galaxy2",
- "0.11.2",
"1.5.1+galaxy0",
+ "0.8.2",
"0.9.1",
"0.14.1.2",
- "0.8.2",
- "0.7.2",
- "0.14.1"
+ "0.14.1",
+ "0.11.2",
+ "0.7.2"
]
},
{
@@ -556677,18 +514361,6 @@
"state": "exact",
"version": "0.14.1.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.10.1+galaxy2",
- "1.5.1+galaxy0",
- "0.14.1",
- "1.10.1+galaxy0",
- "1.9.0+galaxy2",
- "1.3.0+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -556734,6 +514406,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -556790,10 +514466,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -556837,14 +514509,6 @@
"state": "exact",
"version": "0.4.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.6.3",
- "0.6.7+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -556890,6 +514554,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -556947,10 +514615,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557001,9 +514665,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -557014,11 +514678,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557064,6 +514723,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557116,10 +514779,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557167,13 +514826,6 @@
"state": "exact",
"version": "2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557219,6 +514871,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557243,9 +514899,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "2.11.40.8+galaxy0",
"2.11.40.6",
- "2.11.40.4",
- "2.11.40.8+galaxy0"
+ "2.11.40.4"
]
},
{
@@ -557277,10 +514933,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557333,11 +514985,6 @@
"state": "exact",
"version": "2.11.40.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.11.40.6+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557383,6 +515030,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557437,10 +515088,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557493,11 +515140,6 @@
"state": "exact",
"version": "1.7"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557543,6 +515185,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557568,9 +515214,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -557607,10 +515253,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557663,11 +515305,6 @@
"state": "exact",
"version": "1.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557713,6 +515350,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557766,10 +515407,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -557812,11 +515449,6 @@
"state": "exact",
"version": "0.2.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.2.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -557862,6 +515494,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -557914,10 +515550,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -557963,13 +515595,6 @@
"state": "exact",
"version": "2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0.0.8.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -558017,6 +515642,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -558069,10 +515698,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -558115,11 +515740,6 @@
"state": "exact",
"version": "2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -558165,6 +515785,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -558217,10 +515841,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -558263,10 +515883,6 @@
"state": "exact",
"version": "1.7.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -558338,8 +515954,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 312,
- "visitors": 2097078,
+ "visit_duration": 311,
+ "visitors": 2111677,
"workflows": [
{
"creators": [],
@@ -558640,7 +516256,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 0 -->|output| 9;\n 10[\"Trim Galore!\"];\n 0 -->|output| 10;\n 11[\"FastQC\"];\n 1 -->|output| 11;\n 12[\"Trim Galore!\"];\n 1 -->|output| 12;\n 13[\"FastQC\"];\n 2 -->|output| 13;\n 14[\"FastQC\"];\n 4 -->|output| 14;\n 15[\"Salmon quant\"];\n 6 -->|output| 15;\n 2 -->|output| 15;\n 5 -->|output| 15;\n 16[\"Salmon quant\"];\n 6 -->|output| 16;\n 4 -->|output| 16;\n 5 -->|output| 16;\n 17[\"FastQC\"];\n 10 -->|trimmed_reads_single| 17;\n 18[\"MiRDeep2 Mapper\"];\n 10 -->|trimmed_reads_single| 18;\n 19[\"Merge collections\"];\n 11 -->|text_file| 19;\n 9 -->|text_file| 19;\n 20[\"FastQC\"];\n 12 -->|trimmed_reads_single| 20;\n 21[\"MiRDeep2 Mapper\"];\n 12 -->|trimmed_reads_single| 21;\n 22[\"Merge collections\"];\n 13 -->|text_file| 22;\n 14 -->|text_file| 22;\n 23[\"DESeq2\"];\n 15 -->|output_gene_quant| 23;\n 16 -->|output_gene_quant| 23;\n 6 -->|output| 23;\n 24[\"MiRDeep2 Quantifier\"];\n 7 -->|output| 24;\n 3 -->|output| 24;\n 18 -->|output_reads_collapsed| 24;\n 8 -->|output| 24;\n 25[\"MultiQC\"];\n 19 -->|output| 25;\n 26[\"Merge collections\"];\n 20 -->|text_file| 26;\n 17 -->|text_file| 26;\n 27[\"MiRDeep2 Quantifier\"];\n 7 -->|output| 27;\n 3 -->|output| 27;\n 21 -->|output_reads_collapsed| 27;\n 8 -->|output| 27;\n 28[\"MultiQC\"];\n 22 -->|output| 28;\n 29[\"Filter\"];\n 23 -->|deseq_out| 29;\n 30[\"Cut\"];\n 24 -->|miRNAsExpressed| 30;\n 31[\"MultiQC\"];\n 26 -->|output| 31;\n 32[\"Cut\"];\n 27 -->|miRNAsExpressed| 32;\n 33[\"Filter\"];\n 29 -->|out_file1| 33;\n 34[\"Filter\"];\n 29 -->|out_file1| 34;\n 35[\"DESeq2\"];\n 32 -->|out_file1| 35;\n 30 -->|out_file1| 35;\n 36[\"Cut\"];\n 34 -->|out_file1| 36;\n 37[\"Filter\"];\n 35 -->|deseq_out| 37;\n 38[\"Filter FASTA\"];\n 36 -->|out_file1| 38;\n 5 -->|output| 38;\n 39[\"Filter\"];\n 37 -->|out_file1| 39;\n 40[\"Filter\"];\n 37 -->|out_file1| 40;\n 41[\"Cut\"];\n 40 -->|out_file1| 41;\n 42[\"Filter FASTA\"];\n 41 -->|out_file1| 42;\n 8 -->|output| 42;\n 43[\"Filter FASTA\"];\n 41 -->|out_file1| 43;\n 7 -->|output| 43;\n 44[\"Concatenate datasets\"];\n 43 -->|output| 44;\n 42 -->|output| 44;\n 45[\"TargetFinder\"];\n 38 -->|output| 45;\n 44 -->|out_file1| 45;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Plant bulk RNA-Seq workflow",
"outputs": [
{
@@ -559237,114 +516853,7 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n owner: devteam\n revisions: d6694932c5e0\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n owner: iuc\n revisions: e483be1014b6\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n owner: iuc\n revisions: 5efbd15675ca\n tool_panel_section_label: Multiple Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
- "contributions": {
- "authorship": [
- "estebanpw"
- ],
- "reviewing": [
- "shiltemann",
- "deeptivarshney",
- "hexylena",
- "gallardoalba",
- "estebanpw"
- ]
- },
"contributors": [
- {
- "elixir_node": "es",
- "email": "estebanpw@uma.es",
- "id": "estebanpw",
- "joined": "2020-11",
- "name": "Esteban Perez-Wohlfeil",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "deeptivarshney",
- "joined": "2022-12",
- "name": "Deepti Varshney",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
{
"elixir_node": "es",
"email": "estebanpw@uma.es",
@@ -559390,7 +516899,7 @@
"Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
"Learn how to post-process your sequence comparisons"
],
- "pageviews": 6017973,
+ "pageviews": 6040794,
"pub_date": "2021-02-08",
"questions": [
"How can we run pairwise genome comparisons using Galaxy?",
@@ -559408,10 +516917,10 @@
],
"short_id": "T00176",
"short_tools": [
- "tp_awk_tool",
- "clustalw",
"chromeister",
- "gecko"
+ "gecko",
+ "clustalw",
+ "tp_awk_tool"
],
"slides": true,
"slides_recordings": false,
@@ -559468,6 +516977,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -559523,10 +517036,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -559573,11 +517082,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -559622,6 +517126,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -559676,10 +517184,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -559726,11 +517230,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -559776,6 +517275,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -559830,10 +517333,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -559879,11 +517378,6 @@
"state": "exact",
"version": "2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -559929,6 +517423,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -559984,10 +517482,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -560033,13 +517527,6 @@
"state": "exact",
"version": "1.5.a"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.5.a+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -560083,6 +517570,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -560136,10 +517627,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -560183,10 +517670,6 @@
"state": "exact",
"version": "1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -560242,7 +517725,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 286,
- "visitors": 2197227,
+ "visitors": 2207898,
"workflows": [
{
"creators": [],
@@ -560343,7 +517826,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Chromeister\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n 2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n 2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n 2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n 5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n 2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n 2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n 9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n 2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "CHROMEISTER chromosome comparison",
"outputs": [
{
@@ -560659,7 +518142,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Gecko\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n 2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n 3[\"Text reformatting\"];\n 2 -->|alignments2| 3;\n 4[\"ClustalW\"];\n 3 -->|outfile| 4;\n d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n 4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n 4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:34 +0000",
+ "modified": "2024-12-13 13:26:17 +0000",
"name": "GECKO pairwise comparison",
"outputs": [
{
@@ -561016,6 +518499,9 @@
},
{
"avatar": "/training-material/shared/images/logo-dataplant.svg",
+ "funder_name": "DFG",
+ "funding_database": "dfg",
+ "funding_id": "442077441",
"id": "nfdi4plants",
"joined": "2024-07",
"members": [
@@ -561030,7 +518516,7 @@
"name": "DataPLANT (NFDI4Plants)",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
"short_name": "DataPLANT",
- "url": "https://training.galaxyproject.org/training-material/api/organisations/nfdi4plants.json"
+ "url": "https://training.galaxyproject.org/training-material/api/grants/nfdi4plants.json"
},
{
"affiliations": [
@@ -561158,7 +518644,6 @@
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -561187,7 +518672,7 @@
"Load FASTA sequence into Galaxy",
"Perform NCBI-Blast+ analysis against MAdLandDB"
],
- "pageviews": 1553,
+ "pageviews": 1556,
"pub_date": "2023-01-16",
"questions": [
"What is MAdLand DB?",
@@ -561196,8 +518681,8 @@
"short_id": "T00238",
"short_tools": [
"ncbi_blastp_wrapper",
- "ncbi_blastx_wrapper",
- "bg_diamond"
+ "bg_diamond",
+ "ncbi_blastx_wrapper"
],
"slides": false,
"slides_recordings": false,
@@ -561213,11 +518698,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -561269,6 +518749,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -561324,10 +518808,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -561374,11 +518854,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -561423,6 +518898,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -561482,10 +518961,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -561528,11 +519003,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -561578,6 +519048,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -561612,8 +519086,8 @@
"state": "inexact",
"versions": [
"2.10.1+galaxy1",
- "2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.14.1+galaxy2"
]
},
{
@@ -561636,10 +519110,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -561682,8 +519152,8 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.14.1+galaxy2",
"0.3.3",
+ "2.14.1+galaxy2",
"0.0.11",
"0.1.07",
"0.3.0"
@@ -561699,11 +519169,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -561751,6 +519216,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -561784,9 +519253,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.3.3",
+ "2.10.1+galaxy1",
"2.14.1+galaxy2",
- "2.10.1+galaxy1"
+ "0.3.3"
]
},
{
@@ -561809,10 +519278,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -561855,10 +519320,10 @@
"state": "inexact",
"versions": [
"0.3.1",
- "0.3.3",
"2.14.1+galaxy2",
- "0.3.0",
+ "0.3.3",
"0.1.07",
+ "0.3.0",
"0.0.11"
]
},
@@ -561872,11 +519337,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -561934,7 +519394,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 162,
- "visitors": 1218,
+ "visitors": 1220,
"zenodo_link": "https://zenodo.org/records/7524427"
},
{
@@ -561963,7 +519423,8 @@
"StellaEggels"
],
"funding": [
- "nfdi4plants"
+ "nfdi4plants",
+ "dfg"
],
"reviewing": []
},
@@ -562068,6 +519529,9 @@
},
{
"avatar": "/training-material/shared/images/logo-dataplant.svg",
+ "funder_name": "DFG",
+ "funding_database": "dfg",
+ "funding_id": "442077441",
"id": "nfdi4plants",
"joined": "2024-07",
"members": [
@@ -562082,7 +519546,17 @@
"name": "DataPLANT (NFDI4Plants)",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
"short_name": "DataPLANT",
- "url": "https://training.galaxyproject.org/training-material/api/organisations/nfdi4plants.json"
+ "url": "https://training.galaxyproject.org/training-material/api/grants/nfdi4plants.json"
+ },
+ {
+ "avatar": "/training-material/shared/images/DFG_grant.png",
+ "github": false,
+ "id": "dfg",
+ "joined": "2024-12",
+ "name": "Deutsche Forschungsgemeinschaft",
+ "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dfg/",
+ "short_name": "DFG",
+ "url": "https://training.galaxyproject.org/training-material/api/organisations/dfg.json"
}
],
"dir": "topics/fair/tutorials/dataplant-arcs",
@@ -562114,8 +519588,8 @@
],
"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-10-28",
- "pageviews": 175115,
+ "mod_date": "2024-12-11",
+ "pageviews": 197922,
"priority": 2,
"pub_date": "2024-10-22",
"questions": [
@@ -562198,12 +519672,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/dataplant-arcs/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/dataplant-arcs/tutorial.json"
},
- "version": 2,
+ "version": 3,
"video": true,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 388,
- "visitors": 71708,
+ "visit_duration": 386,
+ "visitors": 81433,
"zenodo_link": "https://zenodo.org/records/13970369"
},
{
@@ -562272,20 +519746,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n owner: iuc\n revisions: 55e35e9203cf\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n owner: iuc\n revisions: 9bd945a03d7b\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n owner: iuc\n revisions: aaa5da8e73a9\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n owner: iuc\n revisions: b409c2486353\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n owner: iuc\n revisions: c5d3684f7c4c\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n owner: iuc\n revisions: ab55fe8030b6\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n owner: iuc\n revisions: 6adf98e782f3\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n owner: iuc\n revisions: bf2017df9837\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
- "contributions": {
- "authorship": [
- "mtekman",
- "beatrizserrano",
- "gallardoalba",
- "pavanvidem"
- ],
- "reviewing": [
- "mtekman",
- "nomadscientist",
- "hexylena",
- "beatrizserrano"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -562338,80 +519798,6 @@
"orcid": "0000-0002-5192-126X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "bio": "Senior Lecturer at The Open University",
- "elixir_node": "uk",
- "email": "wendi.bacon@open.ac.uk",
- "fediverse": "https://mstdn.science/@wendibacon1",
- "fediverse_flavor": "mastodon",
- "id": "nomadscientist",
- "joined": "2020-03",
- "matrix": "nomadscientist:matrix.org",
- "name": "Wendi Bacon",
- "orcid": "0000-0002-8170-8806",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
- "twitter": "WendiBacon1",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "email": "beatrizserrano.galaxy@gmail.com",
- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
}
],
"dir": "topics/single-cell/tutorials/scrna-plant",
@@ -562450,7 +519836,7 @@
"Generate a DotPlot emulating the original paper using a different analysis tool",
"Determine robust clusters across scRNA-seq pipelines"
],
- "pageviews": 2618,
+ "pageviews": 2627,
"priority": 3,
"pub_date": "2021-04-08",
"questions": [
@@ -562487,14 +519873,14 @@
],
"short_id": "T00250",
"short_tools": [
- "scanpy_normalize",
- "anndata_manipulate",
- "scanpy_cluster_reduce_dimension",
- "scanpy_plot",
- "anndata_import",
"scanpy_remove_confounders",
+ "scanpy_normalize",
"scanpy_filter",
- "scanpy_inspect"
+ "anndata_import",
+ "scanpy_plot",
+ "anndata_manipulate",
+ "scanpy_inspect",
+ "scanpy_cluster_reduce_dimension"
],
"slides": false,
"slides_recordings": false,
@@ -562557,6 +519943,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -562612,10 +520002,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -562662,11 +520048,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -562711,6 +520092,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -562763,10 +520148,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -562799,12 +520180,12 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy1",
"0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
"0.6.22.post1+galaxy4",
- "0.6.22.post1+galaxy3"
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
+ "0.6.22.post1+galaxy1"
]
},
{
@@ -562819,10 +520200,6 @@
"state": "exact",
"version": "0.7.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -562868,6 +520245,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -562920,10 +520301,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -562956,10 +520333,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -562975,10 +520352,6 @@
"state": "exact",
"version": "0.7.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563024,6 +520397,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563076,10 +520453,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563112,11 +520485,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2",
- "1.4.4+galaxy0"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy1"
]
},
{
@@ -563129,10 +520502,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563178,6 +520547,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563230,10 +520603,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563266,11 +520635,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4+galaxy0",
- "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy1",
"1.4+galaxy0",
- "1.4.4.post1+galaxy2"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
+ "1.4.4.post1+galaxy0"
]
},
{
@@ -563283,10 +520652,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563332,6 +520697,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563384,10 +520753,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563422,9 +520787,9 @@
"versions": [
"1.4.4+galaxy0",
"1.4.4.post1+galaxy0",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy2",
- "1.4+galaxy0"
+ "1.4.4.post1+galaxy2"
]
},
{
@@ -563437,10 +520802,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563486,6 +520847,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563538,10 +520903,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563574,11 +520935,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy2",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy0",
- "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
"1.4.4.post1+galaxy1",
- "1.4+galaxy0"
+ "1.4.4+galaxy0"
]
},
{
@@ -563591,10 +520952,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563640,6 +520997,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563692,10 +521053,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563728,10 +521085,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -563747,10 +521104,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -563799,6 +521152,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -563851,10 +521208,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -563887,10 +521240,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "1.4.4.post1",
"1.4.4.post1+galaxy2",
"1.4.4",
"1.4.4.post1+galaxy1",
- "1.4.4.post1",
"1.4"
]
},
@@ -563904,10 +521257,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -563969,7 +521318,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 82,
- "visitors": 2079,
+ "visitors": 2087,
"workflows": [
{
"creators": [],
@@ -564218,7 +521567,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n style 5 fill:#ded,stroke:#393,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n style 6 fill:#ded,stroke:#393,stroke-width:4px;\n 7[\"Import Anndata and loom\"];\n 1 -->|output| 7;\n 8[\"Import Anndata and loom\"];\n 2 -->|output| 8;\n 9[\"Manipulate AnnData\"];\n 7 -->|anndata| 9;\n 8 -->|anndata| 9;\n 10[\"Rename Batches\"];\n 9 -->|anndata| 10;\n 680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n 10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n 11[\"QC metrics\"];\n 10 -->|anndata| 11;\n 12[\"Filter genes\"];\n 11 -->|anndata_out| 12;\n 3 -->|output| 12;\n 13[\"Plot Violin\"];\n 11 -->|anndata_out| 13;\n 14[\"Filter Cells\"];\n 12 -->|anndata_out| 14;\n 4 -->|output| 14;\n 15[\"Filter Max Features\"];\n 14 -->|anndata_out| 15;\n 5 -->|output| 15;\n 16[\"Filter Max Library Size\"];\n 15 -->|anndata| 16;\n 6 -->|output| 16;\n 17[\"Save RAW\"];\n 16 -->|anndata| 17;\n 18[\"Norm to 1e4\"];\n 17 -->|anndata| 18;\n 19[\"Log1p\"];\n 18 -->|anndata_out| 19;\n 20[\"Regress total counts\"];\n 19 -->|anndata_out| 20;\n 21[\"Scale\"];\n 20 -->|anndata_out| 21;\n 22[\"PCA\"];\n 21 -->|anndata_out| 22;\n 23[\"Neighborhod\"];\n 22 -->|anndata_out| 23;\n 24[\"UMAP\"];\n 23 -->|anndata_out| 24;\n 25[\"Leiden\"];\n 24 -->|anndata_out| 25;\n 0 -->|output| 25;\n 48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n 25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n 26[\"Plot PCA batch\"];\n 24 -->|anndata_out| 26;\n 27[\"Plot UMAP batch\"];\n 24 -->|anndata_out| 27;\n 28[\"Plot UMAP leiden, batch\"];\n 25 -->|anndata_out| 28;\n 29[\"Rename Clusters\"];\n 25 -->|anndata_out| 29;\n 30[\"Complex DotPlot\"];\n 25 -->|anndata_out| 30;\n 31[\"Complex DotPlot with new labels\"];\n 29 -->|anndata| 31;\n 32[\"Plot UMAP with new labels\"];\n 29 -->|anndata| 32;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "scRNA Plant Analysis",
"outputs": [
{
@@ -564733,17 +522082,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: histogram\n owner: devteam\n revisions: 6f134426c2b0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n owner: galaxyp\n revisions: 52ac6fde9a5b\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json",
- "contributions": {
- "authorship": [
- "matthias313",
- "foellmelanie"
- ],
- "reviewing": [
- "bgruening",
- "foellmelanie",
- "subinamehta"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -564771,63 +522109,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
"twitter": "MCFoell",
"url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "email": "subinamehta@gmail.com",
- "id": "subinamehta",
- "joined": "2018-06",
- "linkedin": "subinamehta",
- "matrix": "subinamehta:matrix.org",
- "name": "Subina Mehta",
- "orcid": "0000-0001-9818-0537",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
- "twitter": "Subina_Mehta",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
}
],
"dir": "topics/proteomics/tutorials/DIA_Analysis_MSstats",
@@ -564868,7 +522149,7 @@
"Understanding statistical approaches in proteomic analysis",
"Using MSstats to find significantly dysregulated proteins in a Spike-in dataset"
],
- "pageviews": 1424,
+ "pageviews": 1426,
"pub_date": "2020-12-02",
"questions": [
"How to perform statistical analysis on DIA mass spectrometry data?",
@@ -564886,10 +522167,10 @@
],
"short_id": "T00210",
"short_tools": [
- "Grep1",
"msstats",
- "histogram_rpy",
- "Filter1"
+ "Grep1",
+ "Filter1",
+ "histogram_rpy"
],
"slides": false,
"slides_recordings": false,
@@ -564952,6 +522233,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -565007,10 +522292,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -565057,11 +522338,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -565106,6 +522382,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -565158,10 +522438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -565202,10 +522478,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -565248,6 +522520,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -565300,10 +522576,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -565344,10 +522616,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -565390,6 +522658,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -565442,10 +522714,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -565489,11 +522757,6 @@
"state": "exact",
"version": "1.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -565539,6 +522802,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -565592,10 +522859,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -565641,10 +522904,6 @@
"state": "exact",
"version": "3.20.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -565661,8 +522920,8 @@
"versions": [
"4.0.0+galaxy1",
"3.22.0.1",
- "4.0.0.0",
- "3.22.0.0"
+ "3.22.0.0",
+ "4.0.0.0"
]
},
{
@@ -565706,7 +522965,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 102,
- "visitors": 1060,
+ "visitors": 1062,
"workflows": [
{
"creators": [],
@@ -565859,7 +523118,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"MSstats\"];\n 1 -->|output| 3;\n 2 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Select\"];\n 3 -->|comparison_result| 4;\n 0de65b2c-f62c-4068-8ac0-466e419d495b[\"Output\\nSelect_Ecoli\"];\n 4 --> 0de65b2c-f62c-4068-8ac0-466e419d495b;\n style 0de65b2c-f62c-4068-8ac0-466e419d495b stroke:#2c3143,stroke-width:4px;\n 5[\"Filter\"];\n 4 -->|out_file1| 5;\n 197e8a45-392f-4981-8684-2c8326af4528[\"Output\\nFilter_Ecoli\"];\n 5 --> 197e8a45-392f-4981-8684-2c8326af4528;\n style 197e8a45-392f-4981-8684-2c8326af4528 stroke:#2c3143,stroke-width:4px;\n 6[\"Histogram\"];\n 5 -->|out_file1| 6;\n 04c6287d-fd0d-4780-99b6-cf52ee18e06f[\"Output\\nHistogram_Ecoli\"];\n 6 --> 04c6287d-fd0d-4780-99b6-cf52ee18e06f;\n style 04c6287d-fd0d-4780-99b6-cf52ee18e06f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "DIA_analysis_MSstats",
"outputs": [
{
@@ -566380,7 +523639,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"MSstats\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"Select\"];\n 2 -->|comparison_result| 3;\n 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326[\"Output\\nSelect_Ecoli\"];\n 3 --> 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326;\n style 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326 stroke:#2c3143,stroke-width:4px;\n 4[\"Filter\"];\n 3 -->|out_file1| 4;\n 6997a43a-a17b-418b-bb6d-7d32a6c277ae[\"Output\\nFilter_Ecoli\"];\n 4 --> 6997a43a-a17b-418b-bb6d-7d32a6c277ae;\n style 6997a43a-a17b-418b-bb6d-7d32a6c277ae stroke:#2c3143,stroke-width:4px;\n 5[\"Histogram\"];\n 4 -->|out_file1| 5;\n cf3abac3-8227-4af8-a551-6aeae154a0e4[\"Output\\nHistogram_Ecoli\"];\n 5 --> cf3abac3-8227-4af8-a551-6aeae154a0e4;\n style cf3abac3-8227-4af8-a551-6aeae154a0e4 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "DIA_analysis_MSstats",
"outputs": [
{
@@ -566794,24 +524053,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: tabular_to_fasta\n owner: devteam\n revisions: 0a7799698fe5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mz_to_sqlite\n owner: galaxyp\n revisions: f5c632894818\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json",
- "contributions": {
- "authorship": [
- "subinamehta",
- "timothygriffin",
- "pratikdjagtap",
- "jraysajulga",
- "jj-umn",
- "pravs3683"
- ],
- "reviewing": [
- "shiltemann",
- "subinamehta",
- "nsoranzo",
- "bgruening",
- "hexylena",
- "foellmelanie"
- ]
- },
"contributors": [
{
"email": "subinamehta@gmail.com",
@@ -566868,143 +524109,6 @@
"name": "Praveen Kumar",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "email": "subinamehta@gmail.com",
- "id": "subinamehta",
- "joined": "2018-06",
- "linkedin": "subinamehta",
- "matrix": "subinamehta:matrix.org",
- "name": "Subina Mehta",
- "orcid": "0000-0001-9818-0537",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
- "twitter": "Subina_Mehta",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
}
],
"dir": "topics/proteomics/tutorials/proteogenomics-dbsearch",
@@ -567050,7 +524154,7 @@
"objectives": [
"A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides."
],
- "pageviews": 1999,
+ "pageviews": 2002,
"pub_date": "2018-11-20",
"questions": [
"How to identify variant proteoforms in MS data by searching with the customized Protein database?"
@@ -567080,11 +524184,11 @@
],
"short_id": "T00232",
"short_tools": [
- "search_gui",
- "tab2fasta",
+ "query_tabular",
"mz_to_sqlite",
- "peptide_shaker",
- "query_tabular"
+ "tab2fasta",
+ "search_gui",
+ "peptide_shaker"
],
"slides": false,
"slides_recordings": false,
@@ -567147,6 +524251,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -567202,10 +524310,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -567252,11 +524356,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -567301,6 +524400,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -567355,10 +524458,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -567403,11 +524502,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -567453,6 +524547,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -567505,10 +524603,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -567554,10 +524648,6 @@
"state": "exact",
"version": "2.0.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -567603,6 +524693,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -567655,10 +524749,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -567707,11 +524797,6 @@
"state": "exact",
"version": "1.16.36.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.36.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -567757,6 +524842,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -567809,10 +524898,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -567858,11 +524943,6 @@
"state": "exact",
"version": "3.3.10.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.10.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -567908,6 +524988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -567966,10 +525050,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -568016,18 +525096,6 @@
"state": "exact",
"version": "3.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.1",
- "3.3.0",
- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -568085,7 +525153,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 296,
- "visitors": 1307,
+ "visitors": 1309,
"workflows": [
{
"creators": [],
@@ -568273,7 +525341,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nMGF Collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Search GUI\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n d14f9481-80db-4c15-8afc-6fa38ef61deb[\"Output\\nSearch GUI on input dataset(s)\"];\n 3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;\n style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;\n 4[\"Peptide Shaker\"];\n 3 -->|searchgui_results| 4;\n afe0f1a5-28bb-44bd-b32b-c634aa2154f3[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n 4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;\n style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;\n 5[\"mz to sqlite\"];\n 4 -->|mzidentML| 5;\n 1 -->|output| 5;\n 0 -->|output| 5;\n b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9[\"Output\\nmz to sqlite on input dataset(s)\"];\n 5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;\n style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;\n 6[\"Removing reference proteins\"];\n 4 -->|output_psm| 6;\n 4 -->|output_psm| 6;\n 2 -->|output| 6;\n a06ad5fa-9a00-4867-b976-3745c5e59c80[\"Output\\nRemoving reference proteins\"];\n 6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;\n style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;\n 7[\"Selecting sequence with length >6 and <30\"];\n 6 -->|output| 7;\n b71e5417-2864-4712-b5c1-c90725976baf[\"Output\\nSelecting sequence with length >6 and <30\"];\n 7 --> b71e5417-2864-4712-b5c1-c90725976baf;\n style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;\n 8[\"Peptides for BlastP analysis\"];\n 7 -->|output| 8;\n 1ac3c776-8095-4db1-8518-3643dc081006[\"Output\\nPeptides_for_BlastP_analysis\"];\n 8 --> 1ac3c776-8095-4db1-8518-3643dc081006;\n style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN Proteogemics2 Database Search",
"outputs": [
{
@@ -568903,17 +525971,6 @@
},
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"Clustering",
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"Standardisation and normalisation",
- "Heat map generation",
- "Protein quantification",
- "Tag-based peptide identification",
+ "Visualisation",
"Spectrum calculation",
+ "Tag-based peptide identification",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
"Differential protein expression profiling",
- "Principal component plotting"
+ "Protein quantification",
+ "Heat map generation"
],
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@@ -569061,7 +526044,7 @@
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],
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"msstats",
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"ggplot2_heatmap2",
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"slides_recordings": false,
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"url": "https://hyperbrowser.uio.no/coloc-stats"
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"url": "https://usegalaxy.no/",
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"Using OpenSwathworkflow to analyze HEK-Ecoli Spike-in DIA data"
],
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+ "OpenSwathWorkflow",
"pyprophet_export",
"pyprophet_peptide",
- "pyprophet_protein",
"msconvert",
+ "Grep1",
+ "pyprophet_score",
"pyprophet_merge",
- "OpenSwathWorkflow",
- "pyprophet_score"
+ "pyprophet_protein"
],
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"slides_recordings": false,
@@ -573474,6 +530280,10 @@
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"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://usegalaxy.eu",
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- "usegalaxy": false
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"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -573628,6 +530429,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"state": "exact",
@@ -574671,6 +531443,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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{
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{
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@@ -574981,7 +531745,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 131,
- "visitors": 2398,
+ "visitors": 2403,
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@@ -575165,7 +531929,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "DIA_Analysis_OSW",
"outputs": [
{
@@ -576009,24 +532773,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json",
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@@ -576083,143 +532829,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
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],
"dir": "topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis",
@@ -576263,7 +532872,7 @@
"objectives": [
"How to assign and visualize the genomic localization of these identified novel proteoforms?"
],
- "pageviews": 1979,
+ "pageviews": 1985,
"pub_date": "2018-11-20",
"questions": [
"How to verify the spectra of novel proteoforms?",
@@ -576285,10 +532894,10 @@
],
"short_id": "T00233",
"short_tools": [
- "peptide_genomic_coordinate",
- "pep_pointer",
"ncbi_blastp_wrapper",
- "query_tabular"
+ "query_tabular",
+ "pep_pointer",
+ "peptide_genomic_coordinate"
],
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"slides_recordings": false,
@@ -576351,6 +532960,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -576406,10 +533019,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -576456,11 +533065,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -576505,6 +533109,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -576530,8 +533138,8 @@
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"versions": [
"2.10.1+galaxy2",
- "0.3.1",
- "2.10.1+galaxy0"
+ "2.10.1+galaxy0",
+ "0.3.1"
]
},
{
@@ -576563,10 +533171,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -576615,17 +533219,17 @@
"versions": [
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+ "0.1.00",
+ "0.0.22",
"0.1.08",
+ "0.0.19",
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+ "0.0.20",
"0.2.01",
"0.1.04",
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"0.1.01",
- "0.1.06",
- "0.0.20",
- "0.1.00",
- "0.0.19",
- "0.0.14",
- "0.2.00"
+ "0.0.14"
]
},
{
@@ -576633,11 +533237,6 @@
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},
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- "version": "0.3.3"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -576685,6 +533284,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -576737,10 +533340,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -576786,10 +533385,6 @@
"state": "exact",
"version": "0.1.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -576835,6 +533430,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -576887,10 +533486,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -576936,10 +533531,6 @@
"state": "exact",
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -576985,6 +533576,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -577043,10 +533638,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -577093,18 +533684,6 @@
"state": "exact",
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},
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- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -577160,8 +533739,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 157,
- "visitors": 1351,
+ "visit_duration": 156,
+ "visitors": 1356,
"workflows": [
{
"creators": [],
@@ -577418,7 +533997,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nEdited_Mus_Musculus.GRCm38.86\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\npeptides for blast\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nPSM Report\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nmz_sqlite\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\ngenomic mapping sqlite db\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"NCBI BLAST+ blastp\"];\n 1 -->|output| 5;\n 88461c74-1312-41d5-bd54-e7d7297ccd76[\"Output\\nBLASTP_results\"];\n 5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;\n style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;\n 6[\"PSM_Novel_Peptides\"];\n 5 -->|output1| 6;\n 2 -->|output| 6;\n 29c9a368-a7e6-4e8b-81ca-131f63293093[\"Output\\nPSM_Novel_Peptides\"];\n 6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;\n style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;\n 7[\"Novel_Peptides\"];\n 6 -->|output| 7;\n 56954668-7aac-423a-89af-aecf2b405b94[\"Output\\nNovel_Peptides\"];\n 7 --> 56954668-7aac-423a-89af-aecf2b405b94;\n style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;\n 8[\"Peptide Genomic Coodinate\"];\n 4 -->|output| 8;\n 3 -->|output| 8;\n 7 -->|output| 8;\n 60fd3e41-8cb7-4a49-b585-2a43117e9cf8[\"Output\\nPeptide Genomic Coodinate on input dataset(s)\"];\n 8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;\n style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;\n 9[\"PepPointer\"];\n 8 -->|peptide_bed| 9;\n 0 -->|output| 9;\n 3c410bed-ff79-4774-b75c-48659d291160[\"Output\\nPepPointer on input dataset(s)\"];\n 9 --> 3c410bed-ff79-4774-b75c-48659d291160;\n style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;\n 10[\"Final_Summary_Novel_Peptides\"];\n 9 -->|classified| 10;\n 6 -->|output| 10;\n 50e64c95-cd68-47cb-9e0c-b3714b2f2431[\"Output\\nFinal_Summary_Novel_Peptides\"];\n 10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;\n style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN Proteogemics3 Novel Peptide Analysis",
"outputs": [
{
@@ -578094,25 +534673,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flashlfq\n owner: galaxyp\n revisions: 878f6725c4f3\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n owner: galaxyp\n revisions: 9ec469ff191a\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n owner: galaxyp\n revisions: 209b7c5ee9d7\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n owner: galaxyp\n revisions: 4953dcd7dd39\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n owner: galaxyp\n revisions: 9aaa46d45472\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n owner: galaxyp\n revisions: 75b3b3d0adbf\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json",
- "contributions": {
- "authorship": [
- "subinamehta",
- "timothygriffin",
- "pratikdjagtap",
- "emmaleith",
- "mariecrane"
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- "shiltemann",
- "hexylena",
- "lldelisle",
- "subinamehta",
- "bebatut",
- "malloryfreeberg",
- "bgruening",
- "foellmelanie"
- ]
- },
"contributors": [
{
"email": "subinamehta@gmail.com",
@@ -578160,178 +534720,6 @@
"name": "Marie Crane",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
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- "contact_for_training": true,
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
}
],
"dir": "topics/proteomics/tutorials/metaquantome-data-creation",
@@ -578342,11 +534730,11 @@
"topic_0637"
],
"edam_operation": [
- "Prediction and recognition",
- "Visualisation",
"Formatting",
+ "Visualisation",
"Label-free quantification",
- "Filtering"
+ "Filtering",
+ "Prediction and recognition"
],
"edam_topic": [
"Proteomics",
@@ -578392,7 +534780,7 @@
"objectives": [
"A taxonomy, functional and quantitational analysis of metaproteomic mass spectrometry data."
],
- "pageviews": 1380,
+ "pageviews": 1384,
"pub_date": "2020-10-16",
"questions": [
"How do I perform functional and taxonomy analysis on metaproteomics data?",
@@ -578401,19 +534789,19 @@
],
"short_id": "T00222",
"short_tools": [
+ "Filter1",
+ "Cut1",
+ "tp_replace_in_column",
+ "query_tabular",
+ "msconvert",
"flashlfq",
"Grep1",
- "search_gui",
- "unipept",
"Remove beginning1",
- "tp_replace_in_column",
- "tp_replace_in_line",
- "Filter1",
- "msconvert",
+ "unipept",
+ "search_gui",
"regex1",
- "peptide_shaker",
- "query_tabular",
- "Cut1"
+ "tp_replace_in_line",
+ "peptide_shaker"
],
"slides": false,
"slides_recordings": false,
@@ -578471,6 +534859,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -578526,10 +534918,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -578576,11 +534964,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -578625,6 +535008,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -578677,10 +535064,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -578721,10 +535104,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -578767,6 +535146,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -578819,10 +535202,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -578863,10 +535242,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -578909,6 +535284,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -578961,10 +535340,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
- },
{
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@@ -579005,10 +535380,6 @@
"server": "https://usegalaxy.eu",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
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"state": "local"
@@ -579051,6 +535422,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -579103,10 +535478,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -579147,10 +535518,6 @@
"server": "https://usegalaxy.eu",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -579194,157 +535561,7 @@
"state": "missing"
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{
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- {
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- "state": "exact",
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- "state": "missing"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.1.3"
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- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
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- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
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- "server": "https://galaxy-web.ipk-gatersleben.de",
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- {
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
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- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
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- {
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "version": "1.1.3"
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- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
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- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.1.3"
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- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.3"
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- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
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- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.1.3"
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- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.1.3"
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- "state": "missing"
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- "version": "1.1.3"
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- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -579370,7 +535587,7 @@
{
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"state": "exact",
- "version": "1.1.2"
+ "version": "1.1.3"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -579379,7 +535596,7 @@
{
"server": "https://galaxytrakr.org/",
"state": "exact",
- "version": "1.1.2"
+ "version": "1.1.3"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -579401,10 +535618,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -579439,20 +535652,164 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "1.1.2"
+ "version": "1.1.3"
},
{
"server": "https://usegalaxy.cz/",
"state": "exact",
- "version": "1.1.2"
+ "version": "1.1.3"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "1.1.3"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.1.3"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.1.3"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.1.3"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.1.3"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "1.1.2"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "1.1.2"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
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+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
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},
{
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+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "1.1.2"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.1.2"
},
@@ -579501,6 +535858,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -579553,10 +535914,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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},
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{
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"state": "exact",
@@ -579650,6 +536003,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -579702,10 +536059,6 @@
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{
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@@ -579749,11 +536102,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "3.0.19052.0"
- },
{
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"state": "inexact",
@@ -579810,6 +536158,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -579862,10 +536214,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -579914,11 +536262,6 @@
"state": "exact",
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},
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- "version": "1.16.36.3"
- },
{
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"state": "exact",
@@ -579964,6 +536307,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -580016,10 +536363,6 @@
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{
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@@ -580065,11 +536408,6 @@
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{
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"state": "exact",
@@ -580115,6 +536453,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -580173,10 +536515,6 @@
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{
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"state": "inexact",
@@ -580285,6 +536614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
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{
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{
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"state": "exact",
@@ -580453,6 +536778,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -580507,10 +536836,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -580554,10 +536879,6 @@
"state": "exact",
"version": "4.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -580603,6 +536924,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -580659,10 +536984,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -580713,10 +537034,6 @@
"state": "exact",
"version": "4.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -580769,6 +537086,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -580827,10 +537148,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -580877,18 +537194,6 @@
"state": "exact",
"version": "3.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.1",
- "3.3.0",
- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -580956,7 +537261,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 233,
- "visitors": 794,
+ "visitors": 797,
"workflows": [
{
"creators": [],
@@ -581163,7 +537468,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nExperiment_Design\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nFASTA_db\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"mzml to mgf\"];\n 0 -->|output| 3;\n 4[\"Search GUI\"];\n 2 -->|output| 4;\n 3 -->|output| 4;\n 5[\"Peptide Shaker\"];\n 4 -->|searchgui_results| 5;\n 6[\"Replace Text\"];\n 5 -->|output_psm| 6;\n 7[\"Remove beginning\"];\n 5 -->|output_peptides| 7;\n 8[\"Unipept_lca\"];\n 5 -->|output_peptides| 8;\n 9[\"FlashLFQ\"];\n 1 -->|output| 9;\n 6 -->|outfile| 9;\n 0 -->|output| 9;\n 10[\"Unipept_peptinfo\"];\n 7 -->|out_file1| 10;\n 11[\"Replace Text\"];\n 8 -->|output_tsv| 11;\n 12[\"Regex Find And Replace\"];\n 9 -->|quantifiedPeptides| 12;\n 13[\"selecting EC column\"];\n 10 -->|output_ec_tsv| 13;\n 14[\"filter 5% All_funct\"];\n 10 -->|output_go_tsv| 14;\n 15[\"GO_EC\"];\n 13 -->|out_file1| 15;\n 16[\"GO_BP\"];\n 14 -->|output| 16;\n 17[\"GO_CC\"];\n 14 -->|output| 17;\n 18[\"GO_MF\"];\n 14 -->|output| 18;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "metaQuantome_datacreation_workflow",
"outputs": [
{
@@ -581920,25 +538225,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json",
- "contributions": {
- "authorship": [
- "stortebecker",
- "bgruening"
- ],
- "reviewing": [
- "shiltemann",
- "nsoranzo",
- "bgruening",
- "foellmelanie",
- "bebatut",
- "nekrut",
- "willdurand",
- "blankclemens",
- "stortebecker",
- "njall",
- "hexylena"
- ]
- },
"contributors": [
{
"email": "sigloch+github@mailbox.org",
@@ -581981,204 +538267,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
"twitter": "bjoerngruening",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
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- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "id": "nekrut",
- "joined": "2017-09",
- "name": "Anton Nekrutenko",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
- },
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- "joined": "2017-09",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
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- "email": "blankclemens@gmail.com",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "blankclemens",
- "joined": "2017-09",
- "name": "Clemens Blank",
- "orcid": "0000-0002-1726-2256",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
- },
- {
- "email": "sigloch+github@mailbox.org",
- "former_affiliations": [
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- ],
- "id": "stortebecker",
- "joined": "2017-09",
- "name": "Florian Christoph Sigloch",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
- },
- {
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- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/proteomics/tutorials/ntails",
@@ -582211,7 +538299,7 @@
"objectives": [
"Run an N-TAILS data analysis."
],
- "pageviews": 1007,
+ "pageviews": 1010,
"pub_date": "2017-02-14",
"questions": [
"How can protein N-termini be enriched for LC-MS/MS?",
@@ -582219,19 +538307,19 @@
],
"short_id": "T00226",
"short_tools": [
- "IDConflictResolver",
- "MSGFPlusAdapter",
- "IDMapper",
- "FeatureFinderMultiplex",
+ "HighResPrecursorMassCorrector",
+ "MzTabExporter",
"PeptideIndexer",
- "FalseDiscoveryRate",
+ "FeatureFinderMultiplex",
"ConsensusID",
- "FileFilter",
- "HighResPrecursorMassCorrector",
"IDFilter",
+ "FalseDiscoveryRate",
+ "FileFilter",
+ "IDConflictResolver",
"FileMerger",
- "MzTabExporter",
- "IDMerger"
+ "MSGFPlusAdapter",
+ "IDMerger",
+ "IDMapper"
],
"slides": false,
"slides_recordings": false,
@@ -582262,6 +538350,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -582317,10 +538409,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -582367,11 +538455,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -582416,6 +538499,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -582468,10 +538555,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -582512,10 +538595,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -582558,6 +538637,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -582610,10 +538693,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -582654,10 +538733,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -582700,6 +538775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -582752,10 +538831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -582796,10 +538871,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -582842,6 +538913,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -582894,10 +538969,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -582938,10 +539009,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -582984,6 +539051,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -583036,10 +539107,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -583080,10 +539147,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -583126,6 +539189,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -583178,10 +539245,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -583222,10 +539285,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -583268,6 +539327,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -583320,10 +539383,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -583364,10 +539423,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -583410,6 +539465,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -583462,10 +539521,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -583506,10 +539561,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -583552,6 +539603,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -583604,10 +539659,6 @@
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@@ -583694,6 +539741,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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"state": "missing"
@@ -583836,6 +539879,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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"server": "https://usegalaxy.eu",
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"server": "https://usegalaxy.no/",
"state": "missing"
@@ -583978,6 +540017,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -584030,10 +540073,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -584074,10 +540113,6 @@
"server": "https://usegalaxy.eu",
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@@ -584120,6 +540155,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -584172,10 +540211,6 @@
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@@ -584216,10 +540251,6 @@
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{
"server": "https://usegalaxy.no/",
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@@ -584279,8 +540310,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 84,
- "visitors": 697,
+ "visit_duration": 83,
+ "visitors": 700,
"workflows": [
{
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@@ -584390,7 +540421,7 @@
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"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Tails Triple Dimethyl OpenMS2.1",
"outputs": [
{
@@ -585497,22 +541528,6 @@
},
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"contributors": [
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@@ -585555,171 +541570,6 @@
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],
"dir": "topics/proteomics/tutorials/database-handling",
@@ -585760,7 +541610,7 @@
"objectives": [
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],
- "pageviews": 6889,
+ "pageviews": 6899,
"pub_date": "2017-02-14",
"questions": [
"How to download protein FASTA databases of a certain organism?",
@@ -585770,12 +541620,12 @@
],
"short_id": "T00214",
"short_tools": [
- "addValue",
+ "dbbuilder",
"fasta_merge_files_and_filter_unique_sequences",
- "tab2fasta",
"fasta2tab",
"DecoyDatabase",
- "dbbuilder"
+ "tab2fasta",
+ "addValue"
],
"slides": false,
"slides_recordings": false,
@@ -585833,6 +541683,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -585888,10 +541742,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -585938,11 +541788,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -585987,6 +541832,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -586039,10 +541888,6 @@
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{
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@@ -586083,10 +541928,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -586129,6 +541970,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -586182,10 +542027,6 @@
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{
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"state": "exact",
@@ -586230,11 +542071,6 @@
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- "state": "exact",
- "version": "1.1.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -586280,6 +542116,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -586334,10 +542174,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -586382,11 +542218,6 @@
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{
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"state": "exact",
@@ -586432,6 +542263,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "inexact",
@@ -586588,6 +542414,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -586641,10 +542471,6 @@
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"state": "exact",
@@ -586739,6 +542560,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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@@ -586791,10 +542616,6 @@
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@@ -586839,10 +542660,6 @@
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{
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@@ -586906,7 +542723,7 @@
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"video_view": 0,
"visit_duration": 125,
- "visitors": 4231,
+ "visitors": 4239,
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@@ -586965,7 +542782,7 @@
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"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Proteomics: database handling",
"outputs": [
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@@ -587405,7 +543222,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"Protein Database Downloader\"];\n 1[\"Protein Database Downloader\"];\n 2[\"Protein Database Downloader\"];\n 3[\"Protein Database Downloader\"];\n 4[\"Protein Database Downloader\"];\n 5[\"Protein Database Downloader\"];\n 6[\"Protein Database Downloader\"];\n 7[\"Protein Database Downloader\"];\n 8[\"FASTA-to-Tabular\"];\n 2 -->|output_database| 8;\n 9[\"FASTA Merge Files and Filter Unique Sequences\"];\n 5 -->|output_database| 9;\n 4 -->|output_database| 9;\n 3 -->|output_database| 9;\n 1 -->|output_database| 9;\n 0 -->|output_database| 9;\n 6 -->|output_database| 9;\n 10[\"Add column\"];\n 8 -->|output| 10;\n 11[\"FASTA-to-Tabular\"];\n 9 -->|output| 11;\n 12[\"Tabular-to-FASTA\"];\n 10 -->|out_file1| 12;\n 13[\"Add column\"];\n 11 -->|output| 13;\n 14[\"Tabular-to-FASTA\"];\n 13 -->|out_file1| 14;\n 15[\"FASTA Merge Files and Filter Unique Sequences\"];\n 12 -->|output| 15;\n 7 -->|output_database| 15;\n 14 -->|output| 15;\n 16[\"DecoyDatabase\"];\n 15 -->|output| 16;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Proteomics: database handling including mycoplasma",
"outputs": [
{
@@ -588507,16 +544324,16 @@
],
"dir": "topics/proteomics/tutorials/clinical-mp-2-discovery",
"edam_operation": [
- "Imputation",
- "Visualisation",
"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Formatting",
"Filtering",
- "Heat map generation",
+ "Visualisation",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
+ "Formatting",
"Protein quantification",
- "Principal component plotting"
+ "Heat map generation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -588555,7 +544372,7 @@
"Extract confident peptides and proteins",
"Generate a microbial peptide panel for verification"
],
- "pageviews": 298,
+ "pageviews": 304,
"pub_date": "2024-02-06",
"questions": [
"How to perform database searching?",
@@ -588588,23 +544405,23 @@
],
"short_id": "T00414",
"short_tools": [
- "Grep1",
- "search_gui",
- "fasta_merge_files_and_filter_unique_sequences",
- "dbbuilder",
- "tp_cat",
- "fasta_cli",
- "Remove beginning1",
- "msconvert",
"Filter1",
- "maxquant",
+ "Cut1",
+ "dbbuilder",
"ident_params",
- "fasta2tab",
- "peptide_shaker",
- "filter_tabular",
"query_tabular",
+ "fasta_merge_files_and_filter_unique_sequences",
"Grouping1",
- "Cut1"
+ "tp_cat",
+ "fasta2tab",
+ "msconvert",
+ "Grep1",
+ "Remove beginning1",
+ "filter_tabular",
+ "search_gui",
+ "maxquant",
+ "fasta_cli",
+ "peptide_shaker"
],
"slides": false,
"slides_recordings": false,
@@ -588656,6 +544473,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -588711,10 +544532,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -588761,11 +544578,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -588810,6 +544622,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -588862,10 +544678,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -588906,10 +544718,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -588952,6 +544760,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -589004,10 +544816,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -589048,10 +544856,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -589094,6 +544898,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -589146,10 +544954,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -589190,10 +544994,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -589237,145 +545037,7 @@
"state": "local"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "local"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "local"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "local"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "local"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "local"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "local"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "local"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "local"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "local"
- },
- {
- "id": "Remove beginning1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "local"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -589430,10 +545092,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -589475,7 +545133,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Remove beginning1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -589520,6 +545312,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -589574,10 +545370,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -589626,11 +545418,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -589676,6 +545463,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -589731,10 +545522,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -589781,11 +545568,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -589831,6 +545613,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -589883,10 +545669,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -589932,11 +545714,6 @@
"state": "exact",
"version": "0.3.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -589982,6 +545759,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590035,10 +545816,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -590083,11 +545860,6 @@
"state": "exact",
"version": "1.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -590133,6 +545905,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590185,10 +545961,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590232,10 +546004,6 @@
"state": "exact",
"version": "2.0.3.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -590283,6 +546051,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590335,10 +546107,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590371,8 +546139,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.19052.1",
- "3.0.19052.0"
+ "3.0.19052.0",
+ "3.0.19052.1"
]
},
{
@@ -590385,11 +546153,6 @@
"state": "exact",
"version": "3.0.20287.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.20287.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -590438,6 +546201,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590490,10 +546257,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590536,11 +546299,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -590585,6 +546343,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590637,10 +546399,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590683,11 +546441,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -590732,6 +546485,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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"state": "missing"
@@ -590784,10 +546541,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590834,11 +546587,6 @@
"state": "exact",
"version": "2.0.33+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.33+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -590887,6 +546635,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -590939,10 +546691,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -590989,11 +546737,6 @@
"state": "exact",
"version": "4.0.41+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.41+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -591041,6 +546784,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -591095,10 +546842,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -591145,10 +546888,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -591194,6 +546933,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -591252,10 +546995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -591301,11 +547040,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -591375,7 +547109,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 400,
- "visitors": 211,
+ "visitors": 214,
"workflows": [
{
"creators": [
@@ -591487,7 +547221,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Identification Parameters: PAR file\"];\n 2[\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Human SwissProt reviewed only\"];\n e0de9f90-a710-4b55-af62-41ba1c2d8e1f[\"Output\\nHuman SwissProt (reviewed only)\"];\n 3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;\n style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;\n 4[\"Contaminants cRAP\"];\n 5[\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"];\n 0 -->|output| 6;\n 7[\"msconvert\"];\n 2 -->|output| 7;\n 8[\"Human SwissProt+cRAP\"];\n 3 -->|output_database| 8;\n 4 -->|output_database| 8;\n 2f14902f-b005-4c08-b6d1-6d7ee0b4b199[\"Output\\nHuman SwissProt+cRAP\"];\n 8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;\n style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;\n 9[\"MaxQuant\"];\n 0 -->|output| 9;\n 2 -->|output| 9;\n 5 -->|output| 9;\n 10[\"Search GUI\"];\n 6 -->|input_database_concatenated_target_decoy| 10;\n 1 -->|Identification_Parameters_File| 10;\n 7 -->|output| 10;\n 11[\"FASTA-to-Tabular\"];\n 8 -->|output| 11;\n 12[\"Select microbial peptides MQ\"];\n 9 -->|peptides| 12;\n d7718bab-9e75-4729-bfb6-03bc3112a0e2[\"Output\\nSelect microbial peptides (MQ)\"];\n 12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;\n style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;\n 13[\"Peptide Shaker\"];\n 10 -->|searchgui_results| 13;\n 14[\"Filter Tabular\"];\n 11 -->|output| 14;\n 15[\"MQ Peptide Sequences\"];\n 12 -->|out_file1| 15;\n 16[\"Select microbial peptides SGPS\"];\n 13 -->|output_peptides| 16;\n 14fd9080-df92-4c61-b1f1-3f700a166700[\"Output\\nSelect microbial peptides (SGPS)\"];\n 16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;\n style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;\n 17[\"Select microbial PSMs\"];\n 13 -->|output_psm| 17;\n 18[\"Remove beginning\"];\n 15 -->|out_file1| 18;\n 19[\"Filter confident microbial peptides\"];\n 16 -->|out_file1| 19;\n 1c6c953f-d192-4953-938a-9f401315bc0d[\"Output\\nFilter confident microbial peptides\"];\n 19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;\n style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;\n 20[\"Filter confident microbial PSMs\"];\n 17 -->|out_file1| 20;\n d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2[\"Output\\nFilter confident microbial PSMs\"];\n 20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;\n style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;\n 21[\"MQ Distinct Peptides\"];\n 18 -->|out_file1| 21;\n 07cae017-0b39-4065-b83e-b5f2e27fe740[\"Output\\nMQ Peptides\"];\n 21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;\n style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;\n 22[\"Query Tabular\"];\n 20 -->|out_file1| 22;\n 20 -->|out_file1| 22;\n 14 -->|output| 22;\n 23[\"Cut\"];\n 22 -->|output| 23;\n 24[\"SGPS Distinct Peptides\"];\n 23 -->|out_file1| 24;\n b6c61697-ff52-43c0-8fb4-765d7b4204cc[\"Output\\nSGPS Distinct Peptides\"];\n 24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;\n style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;\n 25[\"SGPS-MQ Peptides\"];\n 21 -->|out_file1| 25;\n 24 -->|out_file1| 25;\n a8c2de2e-e322-4830-9d28-2f79bf937013[\"Output\\nSGPS-MQ Peptides\"];\n 25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;\n style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;\n 26[\"Distinct Peptides\"];\n 25 -->|out_file1| 26;\n ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7[\"Output\\nDistinct Peptides\"];\n 26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;\n style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF2_Discovery-Workflow",
"outputs": [
{
@@ -592325,21 +548059,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json",
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- "foellmelanie",
- "matthias313"
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- "reviewing": [
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- "hexylena",
- "npinter",
- "bgruening",
- "shiltemann",
- "foellmelanie"
- ]
- },
"contributors": [
{
"id": "KlemensFroehlich",
@@ -592374,148 +548093,18 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
"twitter": "mfahrner313",
"url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
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- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "uni-freiburg"
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "uni-freiburg",
- "elixir-europe"
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
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- "linkedin": "shiltemann",
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- "name": "Melanie F\u00f6ll",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
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}
],
"dir": "topics/proteomics/tutorials/maxquant-msstats-tmt",
"edam_operation": [
- "Imputation",
- "Visualisation",
"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Heat map generation",
+ "Visualisation",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
"Protein quantification",
- "Principal component plotting"
+ "Heat map generation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -592545,7 +548134,7 @@
"Learn how to create an experimental design template for fractionated data in MaxQuant",
"Learn how to create an annotation file for MSstatsTMT"
],
- "pageviews": 4949,
+ "pageviews": 4958,
"pub_date": "2021-08-13",
"questions": [
"How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?",
@@ -592607,6 +548196,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -592662,10 +548255,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -592712,11 +548301,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -592762,170 +548346,7 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
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@@ -592981,7 +548402,166 @@
"state": "missing"
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{
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@@ -593028,10 +548608,6 @@
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@@ -593088,7 +548664,7 @@
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"visit_duration": 100,
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@@ -593234,7 +548810,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "MaxQuant MSstatsTMT Training",
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{
@@ -593789,11 +549365,11 @@
],
"dir": "topics/proteomics/tutorials/clinical-mp-1-database-generation",
"edam_operation": [
- "Expression analysis",
+ "Target-Decoy",
+ "de Novo sequencing",
"Tag-based peptide identification",
"Protein identification",
- "Target-Decoy",
- "de Novo sequencing"
+ "Expression analysis"
],
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"exact_supported_servers": [
@@ -593832,7 +549408,7 @@
"For better identification results, combine host and microbial proteins.",
"Reduced database provides better FDR stats."
],
- "pageviews": 593,
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"pub_date": "2024-02-06",
"questions": [
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@@ -593865,10 +549441,10 @@
],
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- "dbbuilder",
"fasta_merge_files_and_filter_unique_sequences",
- "uniprotxml_downloader"
+ "dbbuilder",
+ "uniprotxml_downloader",
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"slides_recordings": false,
@@ -593921,6 +549497,10 @@
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"url": "https://hyperbrowser.uio.no/coloc-stats"
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{
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@@ -593976,10 +549556,6 @@
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@@ -594026,11 +549602,6 @@
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -594075,6 +549646,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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@@ -594127,10 +549702,6 @@
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@@ -594176,11 +549747,6 @@
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@@ -594226,6 +549792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -594279,10 +549849,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "exact",
@@ -594327,11 +549893,6 @@
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"state": "exact",
@@ -594378,149 +549939,7 @@
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- "state": "missing"
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- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -594576,7 +549995,145 @@
"state": "missing"
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{
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
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+ "server": "https://usegalaxy.be/",
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+ "version": "1.9.4+galaxy4"
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+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.9.4+galaxy4"
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+ {
+ "server": "https://usegalaxy.no/",
+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.9.4+galaxy4"
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+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.9.4+galaxy4"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ "version": "1.9.4+galaxy4"
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+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.3.0",
+ "servers": [
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+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
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+ {
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+ "state": "missing"
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+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
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+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ "state": "missing"
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+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
@@ -594621,10 +550178,6 @@
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -594684,8 +550237,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 289,
- "visitors": 350,
+ "visit_duration": 304,
+ "visitors": 356,
"workflows": [
{
"creators": [
@@ -594824,7 +550377,7 @@
],
"license": "CC-BY-4.0",
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF1_Database_Generation_Workflow",
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{
@@ -595127,18 +550680,6 @@
},
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- "contributions": {
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- "foellmelanie"
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- "reviewing": [
- "shiltemann",
- "bgruening",
- "foellmelanie",
- "subinamehta"
- ]
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"contributors": [
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@@ -595166,108 +550707,18 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
"twitter": "MCFoell",
"url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
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- {
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- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
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@@ -596416,6 +551838,10 @@
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@@ -596566,6 +551984,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "missing"
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@@ -596686,8 +552100,8 @@
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+ "2.6+galaxy0",
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]
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@@ -596720,6 +552134,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -596772,10 +552190,6 @@
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@@ -596820,10 +552234,6 @@
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@@ -596886,7 +552296,7 @@
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"video_view": 0,
"visit_duration": 82,
- "visitors": 3929,
+ "visitors": 3944,
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@@ -597070,7 +552480,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "DIA_lib_OSW",
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{
@@ -597753,19 +553163,6 @@
},
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- "combesf",
- "foellmelanie"
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@@ -597799,65 +553196,6 @@
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"url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
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- "bio": "Researcher at Erasmus Medical Center",
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- "elixir_node": "nl",
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- "fediverse_flavor": "mastodon",
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@@ -597869,8 +553207,7 @@
"hands_on": true,
"id": "proteomics/biomarker_selection",
"inexact_supported_servers": [
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- "UseGalaxy.fr"
+ "UseGalaxy.be"
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@@ -597885,7 +553222,7 @@
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],
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+ "pageviews": 1987,
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"questions": [
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],
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- "IDconverter",
- "tp_cut_tool",
- "prot_features",
- "rna_abbased_data",
"Jvenn",
+ "prot_features",
"retr_pepatlas1",
- "retrieve_from_hpa"
+ "IDconverter",
+ "retrieve_from_hpa",
+ "rna_abbased_data",
+ "tp_cut_tool",
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],
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}
]
},
@@ -597943,6 +553275,10 @@
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"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -597998,10 +553334,6 @@
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{
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"url": "https://usegalaxy.no/",
@@ -598097,6 +553424,10 @@
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{
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@@ -598208,16 +553535,6 @@
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@@ -598417,6 +553726,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -598564,6 +553865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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@@ -598712,6 +554006,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -598859,6 +554145,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -599006,6 +554284,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -599058,10 +554340,6 @@
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@@ -599103,13 +554381,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "missing"
@@ -599152,6 +554423,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -599204,10 +554479,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -599252,14 +554523,6 @@
"server": "https://usegalaxy.eu",
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{
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@@ -599318,7 +554581,7 @@
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"video_view": 0,
"visit_duration": 157,
- "visitors": 1440,
+ "visitors": 1444,
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{
"creators": [],
@@ -599356,7 +554619,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"Build tissue-specific expression dataset\"];\n 1[\"Build tissue-specific expression dataset\"];\n 2[\"Filter by keywords and/or numerical value\"];\n 1 -->|output| 2;\n 3[\"Venn diagram\"];\n 0 -->|output| 3;\n 2 -->|kept_lines| 3;\n 4[\"Cut\"];\n 3 -->|output_text| 4;\n 5[\"Filter by keywords and/or numerical value\"];\n 4 -->|output| 5;\n 6[\"Add expression data\"];\n 5 -->|kept_lines| 6;\n 7[\"Filter by keywords and/or numerical value\"];\n 6 -->|output| 7;\n 8[\"ID Converter\"];\n 7 -->|kept_lines| 8;\n 9[\"Add protein features\"];\n 8 -->|output| 9;\n 10[\"Filter by keywords and/or numerical value\"];\n 9 -->|output| 10;\n 11[\"Get MS/MS observations in tissue/fluid\"];\n 10 -->|kept_lines| 11;\n 12[\"Filter by keywords and/or numerical value\"];\n 11 -->|output| 12;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "'Biomarkers4Paris' Workflow",
"outputs": [],
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@@ -599443,24 +554706,6 @@
},
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"contributors": [
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@@ -599503,196 +554748,6 @@
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- "id": "hexylena",
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],
"dir": "topics/proteomics/tutorials/secretome-prediction",
@@ -599722,7 +554777,7 @@
"Predict proteins in the cellular secretome by using WolfPSORT.",
"Combine the results of both predictions."
],
- "pageviews": 879,
+ "pageviews": 880,
"pub_date": "2017-04-13",
"questions": [
"How to predict cellular protein localization based upon GO-terms?",
@@ -599730,18 +554785,18 @@
],
"short_id": "T00235",
"short_tools": [
- "Grep1",
- "tp_easyjoin_tool",
- "get_subontology_from",
+ "Filter1",
"Convert characters1",
- "tp_cut_tool",
+ "tp_easyjoin_tool",
"bg_uniq",
"wolf_psort",
- "Filter1",
+ "Grep1",
+ "uniprot",
+ "tp_cut_tool",
+ "comp1",
"term_id_vs_term_name",
"tp_sorted_uniq",
- "comp1",
- "uniprot"
+ "get_subontology_from"
],
"slides": false,
"slides_recordings": false,
@@ -599772,6 +554827,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -599827,10 +554886,6 @@
"name": "InteractoMIX",
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
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"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -599926,6 +554976,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
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"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -600068,6 +555114,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -600120,10 +555170,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -600164,10 +555210,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -600210,6 +555252,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -600262,10 +555308,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -600306,10 +555348,6 @@
"server": "https://usegalaxy.eu",
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{
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@@ -600352,6 +555390,10 @@
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"server": "https://usegalaxy.eu",
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{
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@@ -600494,6 +555528,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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@@ -600590,10 +555624,6 @@
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@@ -600636,6 +555666,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -600688,10 +555722,6 @@
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@@ -600732,10 +555762,6 @@
"server": "https://usegalaxy.eu",
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{
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@@ -600778,6 +555804,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -600836,10 +555866,6 @@
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{
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@@ -600889,16 +555915,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "9.3+galaxy1",
- "9.3+galaxy2",
- "9.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -600951,6 +555967,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -601009,10 +556029,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -601062,16 +556078,6 @@
"state": "exact",
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
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- "1.1.1",
- "9.3+galaxy0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -601126,6 +556132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -601184,10 +556194,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -601236,15 +556242,6 @@
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},
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "9.3+galaxy1",
- "9.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -601296,6 +556293,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -601348,10 +556349,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -601401,10 +556398,6 @@
"0.6"
]
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -601464,6 +556457,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -601517,10 +556514,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
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@@ -601564,11 +556557,6 @@
"state": "exact",
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- "state": "exact",
- "version": "0.3"
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{
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"state": "missing"
@@ -601611,6 +556599,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -601663,10 +556655,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -601712,10 +556700,6 @@
"state": "exact",
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -601780,8 +556764,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 88,
- "visitors": 577,
+ "visit_duration": 87,
+ "visitors": 578,
"workflows": [
{
"creators": [],
@@ -601923,7 +556907,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"UniProt\"];\n 0 -->|output| 3;\n 4[\"Select\"];\n 1 -->|output| 4;\n 5[\"Get subontology from a given OBO term\"];\n 2 -->|output| 5;\n 6[\"Get subontology from a given OBO term\"];\n 2 -->|output| 6;\n 7[\"Get subontology from a given OBO term\"];\n 2 -->|output| 7;\n 8[\"Get subontology from a given OBO term\"];\n 2 -->|output| 8;\n 9[\"Get subontology from a given OBO term\"];\n 2 -->|output| 9;\n 10[\"WoLF PSORT\"];\n 3 -->|outfile_retrieve_fasta| 10;\n 11[\"Join\"];\n 0 -->|output| 11;\n 4 -->|out_file1| 11;\n 12[\"Get all the term IDs and term names of a given OBO ontology\"];\n 5 -->|output| 12;\n 13[\"Get all the term IDs and term names of a given OBO ontology\"];\n 6 -->|output| 13;\n 14[\"Get all the term IDs and term names of a given OBO ontology\"];\n 7 -->|output| 14;\n 15[\"Get all the term IDs and term names of a given OBO ontology\"];\n 8 -->|output| 15;\n 16[\"Get all the term IDs and term names of a given OBO ontology\"];\n 9 -->|output| 16;\n 17[\"Filter\"];\n 10 -->|tabular_file| 17;\n 18[\"Filter\"];\n 10 -->|tabular_file| 18;\n 19[\"Join\"];\n 12 -->|output| 19;\n 13 -->|output| 19;\n 20[\"Join\"];\n 14 -->|output| 20;\n 15 -->|output| 20;\n 21[\"Join\"];\n 17 -->|out_file1| 21;\n 18 -->|out_file1| 21;\n 22[\"Join\"];\n 19 -->|output| 22;\n 20 -->|output| 22;\n 23[\"Convert\"];\n 21 -->|output| 23;\n 24[\"Join\"];\n 22 -->|output| 24;\n 16 -->|output| 24;\n 25[\"Cut\"];\n 23 -->|out_file1| 25;\n 26[\"Compare two Datasets\"];\n 11 -->|output| 26;\n 24 -->|output| 26;\n 27[\"Unique\"];\n 26 -->|out_file1| 27;\n 28[\"Cut\"];\n 27 -->|outfile| 28;\n 29[\"Join\"];\n 25 -->|output| 29;\n 28 -->|output| 29;\n 30[\"Unique\"];\n 29 -->|output| 30;\n 14e0c6dc-436b-4c4c-9292-d5e00cca8c92[\"Output\\nSecretome proteins\"];\n 30 --> 14e0c6dc-436b-4c4c-9292-d5e00cca8c92;\n style 14e0c6dc-436b-4c4c-9292-d5e00cca8c92 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
"outputs": [
{
@@ -602156,20 +557140,6 @@
},
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- "blankenberg"
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- "reviewing": [
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- "hexylena",
- "bgruening",
- "jaidevjoshi83",
- "subinamehta",
- "foellmelanie"
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"contributors": [
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@@ -602187,133 +557157,6 @@
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"twitter": "dblankenberg",
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- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "erasmusmc"
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- "former_affiliations": [
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- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "twitter": "Subina_Mehta",
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}
],
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@@ -602340,18 +557183,18 @@
"Learn, how to create training data set from features?",
"Assessment of best ML algorithm in predicting anticancer peptide"
],
- "pageviews": 1391,
+ "pageviews": 1393,
"pub_date": "2021-01-22",
"questions": [
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],
"short_id": "T00225",
"short_tools": [
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- "pdaug_addclasslabel",
- "pdaug_sequence_property_based_descriptors",
"pdaug_basic_plots",
- "pdaug_ml_models"
+ "pdaug_sequence_property_based_descriptors",
+ "pdaug_ml_models",
+ "pdaug_merge_dataframes",
+ "pdaug_addclasslabel"
],
"slides": false,
"slides_recordings": false,
@@ -602388,6 +557231,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -602443,10 +557290,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -602493,11 +557336,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -602542,6 +557380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -602594,10 +557436,6 @@
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{
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{
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"state": "missing"
@@ -602685,6 +557519,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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@@ -602782,10 +557616,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "missing"
@@ -602828,6 +557658,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -602880,10 +557714,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -602925,10 +557755,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -602971,6 +557797,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -603023,10 +557853,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -603068,10 +557894,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -603114,6 +557936,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -603166,10 +557992,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -603211,10 +558033,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -603270,7 +558088,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 118,
- "visitors": 911,
+ "visitors": 912,
"workflows": [
{
"creators": [],
@@ -603359,7 +558177,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nACPs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nnon-ACPs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"PDAUG Sequence Property Based Descriptors\"];\n 0 -->|output| 2;\n 3[\"PDAUG Sequence Property Based Descriptors\"];\n 1 -->|output| 3;\n 4[\"PDAUG Add Class Label\"];\n 2 -->|output1| 4;\n 5[\"PDAUG Add Class Label\"];\n 3 -->|output1| 5;\n 6[\"PDAUG Merge Dataframes\"];\n 4 -->|OutFile1| 6;\n 5 -->|OutFile1| 6;\n 7[\"PDAUG ML Models\"];\n 6 -->|output1| 7;\n 8[\"PDAUG ML Models\"];\n 6 -->|output1| 8;\n 9[\"PDAUG ML Models\"];\n 6 -->|output1| 9;\n 10[\"PDAUG ML Models\"];\n 6 -->|output1| 10;\n 11[\"PDAUG ML Models\"];\n 6 -->|output1| 11;\n 12[\"PDAUG ML Models\"];\n 6 -->|output1| 12;\n 13[\"PDAUG Merge Dataframes\"];\n 7 -->|output1| 13;\n 9 -->|output1| 13;\n 8 -->|output1| 13;\n 10 -->|output1| 13;\n 11 -->|output1| 13;\n 12 -->|output1| 13;\n 14[\"PDAUG Basic Plots\"];\n 13 -->|output1| 14;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "PeptideML",
"outputs": [
{
@@ -603807,26 +558625,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 7fdd9119cc4f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n owner: galaxyp\n revisions: 9aaa46d45472\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n owner: iuc\n revisions: b722161a845a\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json",
- "contributions": {
- "authorship": [
- "timothygriffin",
- "pratikdjagtap",
- "jj-umn",
- "blankclemens",
- "subinamehta"
- ],
- "reviewing": [
- "shiltemann",
- "bebatut",
- "pavanvidem",
- "nsoranzo",
- "hexylena",
- "bgruening",
- "subinamehta",
- "foellmelanie",
- "njall"
- ]
- },
"contributors": [
{
"email": "tgriffin@umn.edu",
@@ -603881,188 +558679,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
"twitter": "Subina_Mehta",
"url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "pavanvidem",
- "joined": "2017-09",
- "name": "Pavankumar Videm",
- "orcid": "0000-0002-5192-126X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "subinamehta@gmail.com",
- "id": "subinamehta",
- "joined": "2018-06",
- "linkedin": "subinamehta",
- "matrix": "subinamehta:matrix.org",
- "name": "Subina Mehta",
- "orcid": "0000-0001-9818-0537",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
- "twitter": "Subina_Mehta",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/proteomics/tutorials/metaproteomics",
@@ -604073,8 +558689,8 @@
"topic_0637"
],
"edam_operation": [
- "Prediction and recognition",
- "Visualisation"
+ "Visualisation",
+ "Prediction and recognition"
],
"edam_topic": [
"Proteomics",
@@ -604111,7 +558727,7 @@
"objectives": [
"A taxonomy and functional analysis of metaproteomic mass spectrometry data."
],
- "pageviews": 4024,
+ "pageviews": 4030,
"pub_date": "2017-06-28",
"questions": [
"How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?",
@@ -604134,11 +558750,11 @@
],
"short_id": "T00221",
"short_tools": [
- "search_gui",
- "unipept",
+ "query_tabular",
"sqlite_to_tabular",
- "peptide_shaker",
- "query_tabular"
+ "unipept",
+ "search_gui",
+ "peptide_shaker"
],
"slides": false,
"slides_recordings": false,
@@ -604201,6 +558817,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -604256,10 +558876,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -604306,11 +558922,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -604355,6 +558966,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -604407,10 +559022,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -604459,11 +559070,6 @@
"state": "exact",
"version": "1.16.36.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.36.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -604509,6 +559115,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -604561,10 +559171,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -604610,11 +559216,6 @@
"state": "exact",
"version": "3.3.10.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.10.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -604660,6 +559261,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -604714,10 +559319,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -604761,10 +559362,6 @@
"state": "exact",
"version": "4.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -604810,6 +559407,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -604868,10 +559469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -604918,18 +559515,6 @@
"state": "exact",
"version": "3.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.1",
- "3.3.0",
- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -604975,6 +559560,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -605030,10 +559619,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -605077,10 +559662,6 @@
"state": "exact",
"version": "2.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -605137,8 +559718,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 166,
- "visitors": 2451,
+ "visit_duration": 167,
+ "visitors": 2456,
"workflows": [
{
"creators": [],
@@ -605340,7 +559921,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Search GUI\"];\n 0 -->|output| 3;\n 1 -->|output| 3;\n 7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"Output\\nSearch GUI on input dataset(s)\"];\n 3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n 4[\"Peptide Shaker\"];\n 3 -->|searchgui_results| 4;\n ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n 4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n 5[\"Query Tabular Select Peptides\"];\n 4 -->|output_psm| 5;\n 6[\"Unipept pept2prot\"];\n 5 -->|output| 6;\n 7[\"Unipept lca\"];\n 5 -->|output| 7;\n 8[\"Go Pop2Prot DB\"];\n 2 -->|output| 8;\n 6 -->|output_tsv| 8;\n 6 -->|output_tsv| 8;\n 4 -->|output_psm| 8;\n 9[\"Genera | PSMs | Peptides\"];\n 4 -->|output_psm| 9;\n 7 -->|output_tsv| 9;\n 10[\"GO Terms: Biological Processes\"];\n 8 -->|sqlitedb| 10;\n 11[\"GO Terms: Molecular Functions\"];\n 8 -->|sqlitedb| 11;\n 12[\"GO Terms: Cellular Localization\"];\n 8 -->|sqlitedb| 12;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Metaproteomics_GTN",
"outputs": [
{
@@ -606141,25 +560722,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: peptideshaker\n owner: galaxyp\n revisions: 78fad25eff17\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n owner: galaxyp\n revisions: 78fad25eff17\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.json",
- "contributions": {
- "authorship": [
- "stortebecker",
- "bgruening"
- ],
- "reviewing": [
- "shiltemann",
- "nsoranzo",
- "bgruening",
- "foellmelanie",
- "bebatut",
- "willdurand",
- "blankclemens",
- "stortebecker",
- "subinamehta",
- "njall",
- "hexylena"
- ]
- },
"contributors": [
{
"email": "sigloch+github@mailbox.org",
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"twitter": "bjoerngruening",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "contact_for_training": true,
- "elixir_node": "de",
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- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
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- "id": "stortebecker",
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- "twitter": "Subina_Mehta",
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- "gallantries",
- "by-covid",
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- "elixir-converge"
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- "avans-atgm",
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- "id": "hexylena",
- "joined": "2017-09",
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- "lat": 51.91,
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
}
],
"dir": "topics/proteomics/tutorials/protein-id-sg-ps",
@@ -606431,7 +560791,7 @@
"objectives": [
"Protein identification from LC-MS/MS raw files."
],
- "pageviews": 4315,
+ "pageviews": 4333,
"pub_date": "2017-06-12",
"questions": [
"How to convert LC-MS/MS raw files?",
@@ -606441,9 +560801,9 @@
],
"short_id": "T00229",
"short_tools": [
+ "FileConverter",
"Grep1",
"search_gui",
- "FileConverter",
"PeakPickerHiRes",
"peptide_shaker"
],
@@ -606476,6 +560836,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -606531,10 +560895,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -606581,11 +560941,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -606630,6 +560985,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -606682,10 +561041,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -606726,10 +561081,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -606772,6 +561123,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -606824,10 +561179,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -606868,10 +561219,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -606914,6 +561261,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -606966,10 +561317,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -607010,10 +561357,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -607056,6 +561399,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -607108,10 +561455,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -607157,15 +561500,6 @@
"state": "exact",
"version": "1.11.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0.33+galaxy1",
- "2.0.25+galaxy0",
- "1.16.36.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -607189,11 +561523,11 @@
"state": "inexact",
"versions": [
"2.0.33+galaxy1",
- "2.0.15+galaxy0",
- "2.0.25+galaxy0",
- "2.0.18+galaxy0",
"1.16.36.3",
+ "2.0.25+galaxy0",
+ "2.0.15+galaxy0",
"1.16.4",
+ "2.0.18+galaxy0",
"2.0.9+galaxy0"
]
},
@@ -607227,6 +561561,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -607279,10 +561617,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -607328,15 +561662,6 @@
"state": "exact",
"version": "2.9.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.10.1",
- "4.0.41+galaxy1",
- "4.0.33+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -607360,11 +561685,11 @@
"versions": [
"3.3.10.1",
"4.0.41+galaxy1",
- "4.0.33+galaxy0",
- "4.0.25+galaxy0",
"3.2.13.1",
+ "4.0.33+galaxy0",
"4.0.22+galaxy0",
"3.2.13",
+ "4.0.25+galaxy0",
"4.0.12+galaxy0"
]
},
@@ -607410,8 +561735,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 123,
- "visitors": 2541,
+ "visit_duration": 122,
+ "visitors": 2559,
"workflows": [
{
"creators": [],
@@ -607521,7 +561846,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput: Protein Database\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput: mzML file\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"PeakPickerHiRes\"];\n 1 -->|output| 2;\n 3[\"FileConverter\"];\n 2 -->|param_out| 3;\n 4[\"Search GUI\"];\n 0 -->|output| 4;\n 3 -->|param_out| 4;\n 5[\"Peptide Shaker\"];\n 4 -->|searchgui_results| 5;\n 6[\"Select\"];\n 5 -->|output_proteins| 6;\n 7[\"Select\"];\n 5 -->|output_proteins| 7;\n 8[\"Select\"];\n 7 -->|out_file1| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Peptide And Protein ID Tutorial",
"outputs": [
{
@@ -608004,7 +562329,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"PeakPickerHiRes\"];\n 1 -->|output| 2;\n 3[\"FileConverter\"];\n 2 -->|param_out| 3;\n 4[\"Search GUI\"];\n 0 -->|output| 4;\n 3 -->|param_out| 4;\n 5[\"Peptide Shaker\"];\n 4 -->|searchgui_results| 5;\n 6[\"Select\"];\n 5 -->|output_proteins| 6;\n 7[\"Select\"];\n 5 -->|output_proteins| 7;\n 8[\"Select\"];\n 7 -->|out_file1| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "ProteinID SG PS Tutorial WF datasetCollection",
"outputs": [
{
@@ -608306,26 +562631,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: ddf54b12c295\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n owner: devteam\n revisions: e7ed3c310b74\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n owner: devteam\n revisions: ef2c525bd8cd\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n owner: devteam\n revisions: 0a7799698fe5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bed_to_protein_map\n owner: galaxyp\n revisions: a7c58b43cbaa\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: custom_pro_db\n owner: galaxyp\n revisions: 2c7df0077d28\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n owner: galaxyp\n revisions: f546e7278f04\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare_to_bed\n owner: galaxyp\n revisions: ba5368c19dbd\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n owner: galaxyp\n revisions: 209b7c5ee9d7\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: translate_bed\n owner: galaxyp\n revisions: '038ecf54cbec'\n tool_panel_section_label: Operate on Genomic Intervals\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n owner: iuc\n revisions: 34d29339abab\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare\n owner: iuc\n revisions: 0f710191a66d\n tool_panel_section_label: Filter and Sort\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n owner: iuc\n revisions: a86e80d3c09c\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n owner: iuc\n revisions: b722161a845a\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n owner: iuc\n revisions: 1ebd14235b92\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json",
- "contributions": {
- "authorship": [
- "subinamehta",
- "timothygriffin",
- "pratikdjagtap",
- "jraysajulga",
- "jj-umn",
- "pravs3683"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening",
- "nsoranzo",
- "subinamehta",
- "jj-umn",
- "abretaud",
- "hexylena",
- "foellmelanie"
- ]
- },
"contributors": [
{
"email": "subinamehta@gmail.com",
@@ -608382,187 +562687,16 @@
"name": "Praveen Kumar",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
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- "sfb992",
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- "lon": 7.842609
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- "elixir-converge"
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}
],
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"edam_operation": [
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- "Statistical calculation",
+ "Sequence alignment",
"RNA-Seq analysis",
"Sequence annotation",
"Transcriptome assembly",
- "Sequence alignment"
+ "Statistical calculation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -608604,7 +562738,7 @@
"objectives": [
"Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences."
],
- "pageviews": 8324,
+ "pageviews": 8360,
"pub_date": "2018-11-20",
"questions": [
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@@ -608625,22 +562759,22 @@
],
"short_id": "T00231",
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- "bed_to_protein_map",
+ "tp_replace_in_column",
+ "query_tabular",
+ "gffcompare",
"custom_pro_db",
- "tab2fasta",
+ "stringtie",
+ "freebayes",
"fasta_merge_files_and_filter_unique_sequences",
- "regexColumn1",
"tp_cat",
- "translate_bed",
- "freebayes",
- "tp_replace_in_column",
+ "fasta2tab",
"sqlite_to_tabular",
+ "tab2fasta",
+ "regexColumn1",
"filter_tabular",
- "fasta2tab",
+ "translate_bed",
"hisat2",
- "query_tabular",
- "stringtie",
- "gffcompare",
+ "bed_to_protein_map",
"gffcompare_to_bed"
],
"slides": false,
@@ -608704,6 +562838,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -608759,10 +562897,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -608809,11 +562943,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -608859,157 +562988,7 @@
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- "state": "missing"
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- {
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
@@ -609035,7 +563014,7 @@
{
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"state": "exact",
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+ "version": "0.1.0"
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{
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@@ -609044,7 +563023,7 @@
{
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+ "version": "0.1.0"
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@@ -609066,10 +563045,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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"state": "inexact",
@@ -609104,198 +563079,42 @@
{
"server": "https://usegalaxy.be/",
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+ "version": "0.1.0"
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{
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{
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{
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{
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{
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+ "version": "0.1.0"
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{
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{
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{
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@@ -609317,6 +563136,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -609339,19 +563162,17 @@
},
{
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+ "state": "exact",
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},
{
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- "state": "inexact",
- "versions": [
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- ]
+ "state": "missing"
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{
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"state": "exact",
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+ "version": "1.1.3"
},
{
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@@ -609373,15 +563194,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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{
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"state": "inexact",
"versions": [
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+ "9.3+galaxy1"
]
},
{
@@ -609411,49 +563228,42 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "1.3.1"
+ "version": "1.1.3"
},
{
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- "state": "inexact",
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- ]
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"state": "exact",
- "version": "1.3.1"
+ "version": "1.1.3"
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{
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+ "server": "https://usegalaxy.eu",
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+ "version": "1.1.3"
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{
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+ "version": "1.1.3"
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{
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+ "version": "1.1.3"
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{
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+ "version": "1.1.3"
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{
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}
],
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+ "version": "1.1.3"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
"servers": [
{
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@@ -609475,6 +563285,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
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@@ -609497,8 +563311,7 @@
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{
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+ "state": "missing"
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{
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@@ -609529,10 +563342,6 @@
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{
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@@ -609577,11 +563386,6 @@
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{
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@@ -609605,7 +563409,7 @@
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -610541,6 +564614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -610701,6 +564770,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -610851,6 +564915,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -611005,6 +565064,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -611321,6 +565364,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -611502,7 +565540,7 @@
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"visit_duration": 156,
- "visitors": 4886,
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@@ -611718,7 +565756,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN Proteogenomics1 Database Creation",
"outputs": [
{
@@ -613431,21 +567469,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: encyclopedia_quantify\n owner: galaxyp\n revisions: 4081e4faa4ab\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_quantify\n owner: galaxyp\n revisions: 1c5cbf8f79ce\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n owner: galaxyp\n revisions: 62a718b76f62\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n owner: galaxyp\n revisions: 36880dfd9fa7\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n owner: galaxyp\n revisions: 3cf310697624\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n owner: galaxyp\n revisions: 6153e8ada1ee\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json",
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- "subinamehta",
- "jj-umn",
- "pratikdjagtap",
- "timothygriffin"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening",
- "subinamehta",
- "hexylena"
- ]
- },
"contributors": [
{
"email": "leith023@umn.edu",
@@ -613494,111 +567517,6 @@
"orcid": "0000-0001-6801-2559",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
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- "elixir-europe"
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- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
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- "linkedin": "shiltemann",
- "location": {
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
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- "linkedin": "bgruening",
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- "lon": 7.842609
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- "twitter": "bjoerngruening",
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- "id": "subinamehta",
- "joined": "2018-06",
- "linkedin": "subinamehta",
- "matrix": "subinamehta:matrix.org",
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- "twitter": "Subina_Mehta",
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- "gallantries",
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- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
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],
"dir": "topics/proteomics/tutorials/encyclopedia",
@@ -613636,7 +567554,7 @@
"Understand the purpose and benefits of using a Chromatogram Library for the detection of peptides",
"You can use Bloom's Taxonomy to write effective learning objectives"
],
- "pageviews": 2182,
+ "pageviews": 2188,
"pub_date": "2021-06-21",
"questions": [
"How to perform quantitative analysis using DIA data with the help of EncyclopeDIA?",
@@ -613659,8 +567577,8 @@
"short_id": "T00215",
"short_tools": [
"encyclopedia_quantify",
- "msconvert",
- "encyclopedia_searchtolib"
+ "encyclopedia_searchtolib",
+ "msconvert"
],
"slides": false,
"slides_recordings": false,
@@ -613713,6 +567631,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -613768,10 +567690,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -613818,11 +567736,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -613867,6 +567780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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@@ -613967,10 +567880,6 @@
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@@ -614015,6 +567924,10 @@
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@@ -614115,10 +568024,6 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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@@ -614458,6 +568355,10 @@
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@@ -614510,10 +568411,6 @@
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@@ -614552,8 +568449,8 @@
"state": "inexact",
"versions": [
"3.0.19052.0",
- "0.3.0",
- "3.0.20287.2"
+ "3.0.20287.2",
+ "0.3.0"
]
},
{
@@ -614561,11 +568458,6 @@
"state": "exact",
"version": "3.0.19052.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.19052.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -614614,6 +568506,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -614666,10 +568562,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -614702,8 +568594,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.19052.1",
- "3.0.19052.0"
+ "3.0.19052.0",
+ "3.0.19052.1"
]
},
{
@@ -614716,11 +568608,6 @@
"state": "exact",
"version": "3.0.20287.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.20287.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -614782,7 +568669,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 110,
- "visitors": 1552,
+ "visitors": 1558,
"workflows": [
{
"creators": [
@@ -614964,7 +568851,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nGPF DIA RAW Files Dataset collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nEXPERIMENTAL DIA RAW FILES WIDE\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nSPECTRAL OR PROSIT LIBRARY\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nBACKGROUND PROTEIN FASTA FILE\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Converting RAW to mzml \"];\n 0 -->|output| 4;\n ee41b00e-11e5-4943-96d0-bb64a0dd976c[\"Output\\nGPF_MZML\"];\n 4 --> ee41b00e-11e5-4943-96d0-bb64a0dd976c;\n style ee41b00e-11e5-4943-96d0-bb64a0dd976c stroke:#2c3143,stroke-width:4px;\n 5[\"msconvert\"];\n 1 -->|output| 5;\n 982b3988-74ff-4755-b03f-564fd72adad9[\"Output\\nExperimental-dataset-MZML\"];\n 5 --> 982b3988-74ff-4755-b03f-564fd72adad9;\n style 982b3988-74ff-4755-b03f-564fd72adad9 stroke:#2c3143,stroke-width:4px;\n 6[\"Library searching\"];\n 3 -->|output| 6;\n 2 -->|output| 6;\n 4 -->|output| 6;\n a6ae2431-c813-408e-b67f-4df16f4d9816[\"Output\\nCHROMATOGRAM LIBRARY\"];\n 6 --> a6ae2431-c813-408e-b67f-4df16f4d9816;\n style a6ae2431-c813-408e-b67f-4df16f4d9816 stroke:#2c3143,stroke-width:4px;\n 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6[\"Output\\nLOG\"];\n 6 --> 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6;\n style 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6 stroke:#2c3143,stroke-width:4px;\n 7[\"EncyclopeDIA Quantify\"];\n 3 -->|output| 7;\n 6 -->|elib| 7;\n 5 -->|output| 7;\n 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34[\"Output\\nQuant-LOG\"];\n 7 --> 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34;\n style 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34 stroke:#2c3143,stroke-width:4px;\n 31f9b9fa-9e6c-4531-b207-e6a4547f96a0[\"Output\\nQUANT LIBRARY\"];\n 7 --> 31f9b9fa-9e6c-4531-b207-e6a4547f96a0;\n style 31f9b9fa-9e6c-4531-b207-e6a4547f96a0 stroke:#2c3143,stroke-width:4px;\n a6d58aaf-fd7b-4d14-92ce-c217e2fbad18[\"Output\\nPEPTIDE QUANTITATION OUTPUT\"];\n 7 --> a6d58aaf-fd7b-4d14-92ce-c217e2fbad18;\n style a6d58aaf-fd7b-4d14-92ce-c217e2fbad18 stroke:#2c3143,stroke-width:4px;\n 5cc9b38b-8355-4367-ab3e-382333a73eff[\"Output\\nPROTEIN QUANTITATION OUTPUT\"];\n 7 --> 5cc9b38b-8355-4367-ab3e-382333a73eff;\n style 5cc9b38b-8355-4367-ab3e-382333a73eff stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "EncyclopeDIA-GTN",
"outputs": [
{
@@ -615426,24 +569313,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: histogram\n owner: devteam\n revisions: 6f134426c2b0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n owner: galaxyp\n revisions: c9eff69a7c62\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_featurefindermultiplex\n owner: galaxyp\n revisions: 5e948629bc73\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n owner: galaxyp\n revisions: 658494a2cb00\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n owner: galaxyp\n revisions: 52ba9695e752\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idconflictresolver\n owner: galaxyp\n revisions: c28f13cab67a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmapper\n owner: galaxyp\n revisions: 39caaa778d2e\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n owner: galaxyp\n revisions: 111c3a00136d\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n owner: galaxyp\n revisions: be74a8cd7d66\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_multiplexresolver\n owner: galaxyp\n revisions: fb647b7cf2c1\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n owner: galaxyp\n revisions: dd173849c3d8\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_proteinquantifier\n owner: galaxyp\n revisions: 16026cdb1330\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n owner: galaxyp\n revisions: 9020199dba0a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n owner: galaxyp\n revisions: 7f6a1f27553e\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json",
- "contributions": {
- "authorship": [
- "stortebecker",
- "bgruening",
- "matthias313"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening",
- "nsoranzo",
- "hexylena",
- "foellmelanie",
- "bebatut",
- "stortebecker",
- "willdurand",
- "njall"
- ]
- },
"contributors": [
{
"email": "sigloch+github@mailbox.org",
@@ -615491,190 +569360,14 @@
"affiliations": [
"uni-freiburg"
],
- "email": "matthias.fahrner@uniklinik-freiburg.de",
- "id": "matthias313",
- "joined": "2019-03",
- "name": "Matthias Fahrner",
- "orcid": "0000-0001-7955-2518",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
- "twitter": "mfahrner313",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
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- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
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- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "email": "sigloch+github@mailbox.org",
- "former_affiliations": [
- "uni-freiburg"
- ],
- "id": "stortebecker",
- "joined": "2017-09",
- "name": "Florian Christoph Sigloch",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
- },
- {
- "id": "willdurand",
- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
+ "email": "matthias.fahrner@uniklinik-freiburg.de",
+ "id": "matthias313",
+ "joined": "2019-03",
+ "name": "Matthias Fahrner",
+ "orcid": "0000-0001-7955-2518",
+ "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+ "twitter": "mfahrner313",
+ "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
}
],
"dir": "topics/proteomics/tutorials/protein-quant-sil",
@@ -615710,7 +569403,7 @@
"objectives": [
"MS1 feature quantitation and mapping of quantitations to peptide and protein IDs."
],
- "pageviews": 1697,
+ "pageviews": 1700,
"pub_date": "2017-03-17",
"questions": [
"What are MS1 features?",
@@ -615730,23 +569423,23 @@
],
"short_id": "T00230",
"short_tools": [
- "IDConflictResolver",
- "Grep1",
- "IDMapper",
- "FeatureFinderMultiplex",
+ "IDScoreSwitcher",
"PeptideIndexer",
- "TextExporter",
+ "tp_tail_tool",
+ "FeatureFinderMultiplex",
+ "ProteinQuantifier",
"FalseDiscoveryRate",
+ "IDConflictResolver",
+ "XTandemAdapter",
"histogram_rpy",
"FidoAdapter",
- "IDPosteriorErrorProbability",
- "ProteinQuantifier",
- "XTandemAdapter",
- "MultiplexResolver",
- "tp_tail_tool",
"FileInfo",
- "IDScoreSwitcher",
- "Summary_Statistics1"
+ "Grep1",
+ "TextExporter",
+ "MultiplexResolver",
+ "Summary_Statistics1",
+ "IDMapper",
+ "IDPosteriorErrorProbability"
],
"slides": false,
"slides_recordings": false,
@@ -615799,6 +569492,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -615854,10 +569551,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -615904,11 +569597,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -615953,6 +569641,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -616005,10 +569697,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -616049,10 +569737,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -616095,6 +569779,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -616147,10 +569835,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -616191,10 +569875,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -616237,6 +569917,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -616291,10 +569975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -616341,11 +570021,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -616391,6 +570066,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -616443,10 +570122,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -616490,11 +570165,6 @@
"state": "exact",
"version": "1.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -616540,6 +570210,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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@@ -616593,7 +570267,157 @@
"state": "missing"
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{
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
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+ "state": "missing"
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+ {
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+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
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+ {
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+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
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+ "2.2.0"
+ ]
+ },
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+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
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+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
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+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "2.3.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "inexact",
+ "versions": [
+ "2.8+galaxy0",
+ "3.1+galaxy0"
+ ]
+ },
+ {
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@@ -616628,7 +570452,6 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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"2.1.0"
]
},
@@ -616644,10 +570467,6 @@
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{
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@@ -616676,7 +570495,7 @@
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},
{
- "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
+ "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
"servers": [
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@@ -616699,160 +570518,7 @@
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- "state": "missing"
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- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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},
{
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"server": "http://galaxy.interactomix.com/",
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@@ -616958,10 +570620,6 @@
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{
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"state": "inexact",
@@ -617008,6 +570666,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -617060,10 +570722,6 @@
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{
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{
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"state": "inexact",
@@ -617161,6 +570815,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -617213,10 +570871,6 @@
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@@ -617264,10 +570918,6 @@
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@@ -617314,6 +570964,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -617366,10 +571020,6 @@
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{
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"state": "inexact",
@@ -617471,6 +571117,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -617523,10 +571173,6 @@
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{
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@@ -617574,10 +571220,6 @@
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -617624,6 +571266,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -617676,10 +571322,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -617727,10 +571369,6 @@
"state": "exact",
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},
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- "state": "missing"
- },
{
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"state": "inexact",
@@ -617777,6 +571415,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -617829,10 +571471,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -617877,10 +571515,6 @@
"state": "exact",
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},
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -617897,8 +571531,8 @@
"state": "inexact",
"versions": [
"2.8+galaxy0",
- "2.6+galaxy0",
- "2.3.0"
+ "2.3.0",
+ "2.6+galaxy0"
]
},
{
@@ -617931,6 +571565,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -617983,10 +571621,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -618019,8 +571653,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.2.0",
- "2.1.0"
+ "2.1.0",
+ "2.2.0"
]
},
{
@@ -618035,10 +571669,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -618089,6 +571719,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -618141,10 +571775,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -618189,10 +571819,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -618239,6 +571865,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -618291,10 +571921,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -618339,10 +571965,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -618389,6 +572011,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -618441,10 +572067,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -618492,10 +572114,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -618567,7 +572185,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 99,
- "visitors": 1181,
+ "visitors": 1184,
"workflows": [
{
"creators": [],
@@ -618738,7 +572356,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nmzml raw file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nfasta file\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FeatureFinderMultiplex\"];\n 0 -->|output| 2;\n 3[\"XTandemAdapter\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"FileInfo\"];\n 3 -->|out| 4;\n 5[\"PeptideIndexer\"];\n 1 -->|output| 5;\n 3 -->|out| 5;\n 6[\"IDPosteriorErrorProbability\"];\n 5 -->|out| 6;\n 7[\"FalseDiscoveryRate\"];\n 6 -->|out| 7;\n 8[\"IDScoreSwitcher\"];\n 7 -->|out| 8;\n 9[\"FileInfo\"];\n 8 -->|out| 9;\n 10[\"FidoAdapter\"];\n 8 -->|out| 10;\n 11[\"FalseDiscoveryRate\"];\n 10 -->|out| 11;\n 12[\"FileInfo\"];\n 11 -->|out| 12;\n 13[\"TextExporter\"];\n 11 -->|out| 13;\n 14[\"IDMapper\"];\n 11 -->|out| 14;\n 2 -->|out_multiplets| 14;\n 15[\"Select\"];\n 13 -->|out| 15;\n 16[\"Select\"];\n 13 -->|out| 16;\n 17[\"IDConflictResolver\"];\n 14 -->|out| 17;\n 18[\"MultiplexResolver\"];\n 17 -->|out| 18;\n 19[\"ProteinQuantifier\"];\n 18 -->|out| 19;\n 11 -->|out| 19;\n 20[\"Summary Statistics\"];\n 19 -->|out| 20;\n 21[\"Select last\"];\n 19 -->|out| 21;\n 22[\"Histogram\"];\n 21 -->|outfile| 22;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
"outputs": [
{
@@ -619961,19 +573579,6 @@
},
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"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Heat map generation",
- "Protein quantification",
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+ "Visualisation",
"Spectrum calculation",
+ "Tag-based peptide identification",
+ "Imputation",
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+ "Statistical calculation",
"Differential protein expression profiling",
- "Principal component plotting"
+ "Protein quantification",
+ "Heat map generation"
],
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"exact_supported_servers": [
@@ -620145,7 +573652,7 @@
"objectives": [
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],
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@@ -620154,14 +573661,14 @@
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- "Add_a_column1",
"tp_sort_header_tool",
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+ "Filter1",
+ "Cut1",
"msstats",
- "Cut1"
+ "Add_a_column1",
+ "histogram_rpy",
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],
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"slides_recordings": false,
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"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://usegalaxy.no/",
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@@ -621781,7 +575248,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Proteomics: MaxQuant workflow",
"outputs": [
{
@@ -622524,20 +575991,6 @@
},
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- "hexylena",
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@@ -622583,157 +576036,6 @@
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- "elixir-europe"
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- "fediverse": "https://fosstodon.org/@bgruening",
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],
"dir": "topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data",
@@ -622754,7 +576056,6 @@
"id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -622776,7 +576077,7 @@
"Getting an overview of the MSI data with the MSI quality control tool",
"How to export MSI data as tabular files"
],
- "pageviews": 3728,
+ "pageviews": 3733,
"pub_date": "2018-11-27",
"questions": [
"Did the tryptic digestions work?",
@@ -622786,9 +576087,9 @@
"short_id": "T00217",
"short_tools": [
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+ "tp_sort_header_tool",
"cardinal_data_exporter",
- "cardinal_quality_report",
- "tp_sort_header_tool"
+ "cardinal_quality_report"
],
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@@ -622812,11 +576113,6 @@
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -622851,6 +576147,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -622906,10 +576206,6 @@
"name": "InteractoMIX",
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},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -622956,11 +576252,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -623005,6 +576296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -623057,10 +576352,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -623101,10 +576392,6 @@
"server": "https://usegalaxy.eu",
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -623147,6 +576434,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -623201,10 +576492,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -623251,11 +576538,6 @@
"state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -623301,6 +576583,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -623353,10 +576639,6 @@
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{
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@@ -623402,14 +576684,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -623461,6 +576735,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -623513,10 +576791,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -623562,14 +576836,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -623588,8 +576854,8 @@
"versions": [
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"2.10.0.0",
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- "3.4.3+galaxy0"
+ "3.4.3+galaxy0",
+ "1.12.1.4"
]
},
{
@@ -623634,7 +576900,7 @@
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"video_view": 0,
"visit_duration": 102,
- "visitors": 2329,
+ "visitors": 2331,
"workflows": [
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@@ -623732,7 +576998,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "MS Imaging Loading Exploring Data",
"outputs": [],
"parent_id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
@@ -623978,14 +577244,14 @@
],
"dir": "topics/proteomics/tutorials/clinical-mp-4-quantitation",
"edam_operation": [
- "Imputation",
- "Visualisation",
"Clustering",
- "Statistical calculation",
"Standardisation and normalisation",
- "Heat map generation",
+ "Visualisation",
+ "Imputation",
+ "Principal component plotting",
+ "Statistical calculation",
"Protein quantification",
- "Principal component plotting"
+ "Heat map generation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -624024,7 +577290,7 @@
"objectives": [
"Perform quantitation using MaxQuant and extract microbial and human proteins and peptides."
],
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+ "pageviews": 152,
"pub_date": "2024-02-06",
"questions": [
"How to perform quantitation?"
@@ -624056,10 +577322,10 @@
],
"short_id": "T00416",
"short_tools": [
- "Grep1",
- "maxquant",
"Grouping1",
- "Cut1"
+ "Grep1",
+ "Cut1",
+ "maxquant"
],
"slides": false,
"slides_recordings": false,
@@ -624122,6 +577388,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -624177,10 +577447,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -624227,11 +577493,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -624276,6 +577537,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -624328,10 +577593,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -624372,10 +577633,6 @@
"server": "https://usegalaxy.eu",
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},
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{
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"state": "local"
@@ -624419,145 +577676,7 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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@@ -624612,10 +577731,6 @@
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@@ -624657,7 +577772,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Grouping1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -624702,6 +577951,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -624754,10 +578007,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -624790,12 +578039,12 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.6.10.43+galaxy1",
"2.0.3.0+galaxy0",
- "1.6.10.43+galaxy3",
+ "1.6.17.0+galaxy3",
"1.6.3.4+galaxy1",
- "1.6.3.4",
- "1.6.17.0+galaxy3"
+ "1.6.10.43+galaxy3",
+ "1.6.10.43+galaxy1",
+ "1.6.3.4"
]
},
{
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"state": "exact",
"version": "1.6.17.0+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
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"state": "inexact",
@@ -624872,7 +578117,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 317,
- "visitors": 104,
+ "visitors": 105,
"workflows": [
{
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@@ -624991,7 +578236,7 @@
],
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF4_Quantitation_Workflow",
"outputs": [],
"parent_id": "proteomics/clinical-mp-4-quantitation",
@@ -625315,7 +578560,7 @@
"objectives": [
"Verification of peptides helps in confirming the presence of the peptides in our samplle"
],
- "pageviews": 167,
+ "pageviews": 169,
"pub_date": "2024-02-06",
"questions": [
"Why do we need to verify our identified peptides",
@@ -625348,17 +578593,17 @@
],
"short_id": "T00415",
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- "dbbuilder",
- "tp_cat",
- "Remove beginning1",
- "collapse_dataset",
- "Filter1",
"pepquery2",
+ "Filter1",
+ "Cut1",
+ "dbbuilder",
"query_tabular",
+ "collapse_dataset",
+ "fasta_merge_files_and_filter_unique_sequences",
"Grouping1",
- "Cut1",
- "uniprotxml_downloader"
+ "tp_cat",
+ "uniprotxml_downloader",
+ "Remove beginning1"
],
"slides": false,
"slides_recordings": false,
@@ -625411,6 +578656,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -625466,10 +578715,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -625516,11 +578761,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -625565,6 +578805,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -625617,10 +578861,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "local"
- },
{
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@@ -625661,10 +578901,6 @@
"server": "https://usegalaxy.eu",
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},
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- "state": "local"
- },
{
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"state": "local"
@@ -625707,6 +578943,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -625759,10 +578999,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -625803,10 +579039,6 @@
"server": "https://usegalaxy.eu",
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},
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- "state": "local"
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{
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"state": "local"
@@ -625849,6 +579081,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -625901,10 +579137,6 @@
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -625945,10 +579177,6 @@
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- "state": "local"
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{
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"state": "local"
@@ -625991,6 +579219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -626043,10 +579275,6 @@
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -626087,10 +579315,6 @@
"server": "https://usegalaxy.eu",
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},
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- "state": "local"
- },
{
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"state": "local"
@@ -626133,6 +579357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626187,10 +579415,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -626239,11 +579463,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -626289,6 +579508,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626341,10 +579564,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
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{
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@@ -626390,11 +579609,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.3.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -626440,6 +579654,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626493,10 +579711,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -626541,11 +579755,6 @@
"state": "exact",
"version": "1.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -626591,6 +579800,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626643,10 +579856,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -626689,10 +579898,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -626741,6 +579946,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626793,10 +580002,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -626839,10 +580044,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -626888,6 +580089,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -626946,10 +580151,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -626995,11 +580196,6 @@
"state": "exact",
"version": "3.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -627045,6 +580241,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -627099,10 +580299,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -627150,11 +580346,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -627218,7 +580409,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 506,
- "visitors": 120,
+ "visitors": 122,
"workflows": [
{
"creators": [
@@ -627357,7 +580548,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"Human UniProt+Isoforms FASTA\"];\n 4bdae9fb-eb48-4821-a806-e7dd3a8c7101[\"Output\\nHuman UniProt+Isoforms FASTA\"];\n 0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;\n style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;\n 1[\"cRAP\"];\n 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa[\"Output\\ncRAP\"];\n 1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;\n style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"Human UniProt+Isoforms+cRAP FASTA\"];\n 0 -->|output_database| 6;\n 1 -->|output_database| 6;\n 62c376eb-85a3-4976-8024-bd72ac528af3[\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"];\n 6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;\n style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;\n 7[\"Cut\"];\n 3 -->|output| 7;\n 8[\"Cut\"];\n 5 -->|output| 8;\n 9[\"PepQuery2\"];\n 6 -->|output| 9;\n 4 -->|output| 9;\n 2 -->|output| 9;\n 10[\"Remove beginning\"];\n 7 -->|out_file1| 10;\n 11[\"Remove beginning\"];\n 8 -->|out_file1| 11;\n 12[\"Collapse Collection\"];\n 9 -->|psm_rank_txt| 12;\n 13[\"Concatenate datasets\"];\n 10 -->|out_file1| 13;\n 11 -->|out_file1| 13;\n 14[\"Filter\"];\n 12 -->|output| 14;\n 15[\"Remove beginning\"];\n 14 -->|out_file1| 15;\n 16[\"Cut\"];\n 15 -->|out_file1| 16;\n 17[\"Peptide and Protein from Peptide reports\"];\n 16 -->|out_file1| 17;\n 13 -->|out_file1| 17;\n bc4e33da-4064-4b78-bb15-5732b08b9316[\"Output\\nPeptide and Protein from Peptide reports\"];\n 17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;\n style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;\n 18[\"Remove beginning\"];\n 17 -->|output| 18;\n 19[\"Group\"];\n 18 -->|out_file1| 19;\n 20[\"Uniprot-ID from verified Peptides\"];\n 19 -->|out_file1| 20;\n cd6c81d8-1f44-4129-b505-2ee4dde10cd2[\"Output\\nUniprot-ID from verified Peptides\"];\n 20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;\n style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;\n 21[\"UniProt\"];\n 20 -->|output| 21;\n 22[\"Quantitation Database for MaxQuant\"];\n 0 -->|output_database| 22;\n 1 -->|output_database| 22;\n 21 -->|proteome| 22;\n a52b5136-db74-496f-9b66-ec1064f2301d[\"Output\\nQuantitation Database for MaxQuant\"];\n 22 --> a52b5136-db74-496f-9b66-ec1064f2301d;\n style a52b5136-db74-496f-9b66-ec1064f2301d stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF3_VERIFICATION_WORKFLOW",
"outputs": [
{
@@ -627814,24 +581005,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n owner: galaxyp\n revisions: 7c45aa1c9464\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_db\n owner: galaxyp\n revisions: e63db1aa82ee\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n owner: galaxyp\n revisions: eb65ab160a10\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n owner: galaxyp\n revisions: 767c1d761aaf\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n owner: galaxyp\n revisions: 7d1c20b315ff\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n owner: galaxyp\n revisions: 35cc7ca0bdc7\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n owner: galaxyp\n revisions: 49a957fb353a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n owner: galaxyp\n revisions: 06f6826d380c\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n owner: galaxyp\n revisions: 982a442a98dd\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n owner: galaxyp\n revisions: b9d453dca8d3\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n owner: galaxyp\n revisions: 02da24eac445\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n owner: galaxyp\n revisions: 8bd7734309f6\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "malloryfreeberg",
- "bgruening",
- "foellmelanie"
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"contributors": [
{
"email": "subinamehta@gmail.com",
@@ -627887,130 +581060,6 @@
"name": "Praveen Kumar",
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"url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
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- "elixir-europe"
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- "gallantries",
- "erasmusmc"
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- "elixir-europe"
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- "twitter": "bebatut",
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- "linkedin": "subinamehta",
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- "twitter": "Subina_Mehta",
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
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- "fediverse": "https://fosstodon.org/@bgruening",
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- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
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- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
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- "twitter": "MCFoell",
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}
],
"dir": "topics/proteomics/tutorials/metaquantome-function",
@@ -628022,16 +581071,16 @@
"topic_3174"
],
"edam_operation": [
- "Visualisation",
+ "Principal component visualisation",
+ "Filtering",
+ "Functional clustering",
"Heat map generation",
+ "Quantification",
"Differential protein expression analysis",
"Statistical inference",
+ "Visualisation",
"Indexing",
- "Quantification",
- "Filtering",
- "Query and retrieval",
- "Principal component visualisation",
- "Functional clustering"
+ "Query and retrieval"
],
"edam_topic": [
"Proteomics",
@@ -628085,7 +581134,7 @@
"objectives": [
"A functional and quantitational analysis of metaproteomic mass spectrometry data."
],
- "pageviews": 527,
+ "pageviews": 533,
"pub_date": "2020-10-29",
"questions": [
"How do I look at differentially expressed proteins?",
@@ -628103,12 +581152,12 @@
],
"short_id": "T00223",
"short_tools": [
- "metaquantome_viz",
+ "metaquantome_filter",
"metaquantome_expand",
"metaquantome_db",
- "metaquantome_filter",
- "metaquantome_stat",
- "metaquantome_sample"
+ "metaquantome_viz",
+ "metaquantome_sample",
+ "metaquantome_stat"
],
"slides": false,
"slides_recordings": false,
@@ -628166,6 +581215,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -628221,10 +581274,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -628271,11 +581320,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -628321,159 +581365,7 @@
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -628528,10 +581420,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -628562,24 +581450,20 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
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+ "state": "exact",
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{
"server": "https://usegalaxy.cz/",
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+ "state": "inexact",
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},
{
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"state": "exact",
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+ "version": "2.0.0-0"
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@@ -628594,18 +581478,23 @@
},
{
"server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.0.2+galaxy0"
+ "state": "inexact",
+ "versions": [
+ "2.0.2+galaxy0",
+ "2.0.1+galaxy0",
+ "2.0.0-2",
+ "2.0.0-1"
+ ]
},
{
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},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -628627,6 +581516,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -628679,10 +581572,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -628713,24 +581602,20 @@
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{
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- {
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"state": "inexact",
"versions": [
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+ "2.0.0-0"
]
},
{
- "server": "https://usegalaxy.eu",
+ "server": "https://usegalaxy.cz/",
"state": "exact",
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+ "version": "2.0.2+galaxy0"
},
{
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- "state": "missing"
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.0.2+galaxy0"
},
{
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@@ -628745,23 +581630,18 @@
},
{
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- "versions": [
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- "2.0.0-2",
- "2.0.1+galaxy0",
- "2.0.0-1"
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+ "state": "exact",
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},
{
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"state": "missing"
}
],
- "version": "2.0.0-0"
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},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -628783,6 +581663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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"mermaid": "flowchart TD\n 0[\"metaQuantome: database\"];\n 1[\"metaQuantome: create samples file\"];\n 2[\"\u2139\ufe0f Input Dataset\\nFunctional file\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nIntensity file\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"metaQuantome: expand\"];\n 0 -->|outfile| 4;\n 3 -->|output| 4;\n 2 -->|output| 4;\n 1 -->|samples_file| 4;\n 5[\"metaQuantome: filter\"];\n 4 -->|outfile| 5;\n 1 -->|samples_file| 5;\n 6[\"metaQuantome: stat\"];\n 5 -->|outfile| 6;\n 1 -->|samples_file| 6;\n 7[\"T2-Bar-Plot\"];\n 6 -->|outfile| 7;\n 6 -->|outfile| 7;\n 8[\"T4-Bar-Plot\"];\n 6 -->|outfile| 8;\n 1 -->|samples_file| 8;\n 9[\"T7-Bar-Plot\"];\n 6 -->|outfile| 9;\n 1 -->|samples_file| 9;\n 10[\"T7-T2-Volcano-Plot\"];\n 6 -->|outfile| 10;\n 1 -->|samples_file| 10;\n 11[\"T4-T2-Volcano-Plot\"];\n 6 -->|outfile| 11;\n 1 -->|samples_file| 11;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "metaquantome-function-worklow",
"outputs": [
{
@@ -631057,23 +584053,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n owner: galaxyp\n revisions: 3cf310697624\n tool_panel_section_label: Convert Formats\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_consensusid\n owner: galaxyp\n revisions: 4e77b8f12cd3\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n owner: galaxyp\n revisions: f7fef900f5b2\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n owner: galaxyp\n revisions: c9eff69a7c62\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n owner: galaxyp\n revisions: 890025d6e426\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n owner: galaxyp\n revisions: 658494a2cb00\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n owner: galaxyp\n revisions: 5ad830edc021\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n owner: galaxyp\n revisions: 52ba9695e752\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idfilter\n owner: galaxyp\n revisions: 382cde407f81\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmerger\n owner: galaxyp\n revisions: 1c5f31b8d632\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n owner: galaxyp\n revisions: c69f69d7867a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n owner: galaxyp\n revisions: 111c3a00136d\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n owner: galaxyp\n revisions: 476b5e296979\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n owner: galaxyp\n revisions: be74a8cd7d66\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_msgfplusadapter\n owner: galaxyp\n revisions: a407b6790342\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peakpickerhires\n owner: galaxyp\n revisions: 3d8d4ada5405\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n owner: galaxyp\n revisions: e039cc5c7aed\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n owner: galaxyp\n revisions: dd173849c3d8\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n owner: galaxyp\n revisions: 9020199dba0a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n owner: galaxyp\n revisions: c8b225c69a7f\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n owner: galaxyp\n revisions: 7f6a1f27553e\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json",
- "contributions": {
- "authorship": [
- "stortebecker",
- "bgruening"
- ],
- "reviewing": [
- "shiltemann",
- "nsoranzo",
- "bgruening",
- "bebatut",
- "hexylena",
- "foellmelanie",
- "blankclemens",
- "stortebecker",
- "njall"
- ]
- },
"contributors": [
{
"email": "sigloch+github@mailbox.org",
@@ -631116,189 +584095,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
"twitter": "bjoerngruening",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
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- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
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- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "elixir-europe",
- "elixir-converge"
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- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
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- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "affiliations": [
- "uni-freiburg"
- ],
- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
- },
- {
- "elixir_node": "de",
- "email": "blankclemens@gmail.com",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "blankclemens",
- "joined": "2017-09",
- "name": "Clemens Blank",
- "orcid": "0000-0002-1726-2256",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
- },
- {
- "email": "sigloch+github@mailbox.org",
- "former_affiliations": [
- "uni-freiburg"
- ],
- "id": "stortebecker",
- "joined": "2017-09",
- "name": "Florian Christoph Sigloch",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/proteomics/tutorials/protein-id-oms",
@@ -631343,7 +584139,7 @@
"objectives": [
"Protein identification from LC-MS/MS raw files."
],
- "pageviews": 5135,
+ "pageviews": 5141,
"pub_date": "2017-10-16",
"questions": [
"How to convert LC-MS/MS raw files?",
@@ -631362,21 +584158,21 @@
],
"short_id": "T00228",
"short_tools": [
- "Grep1",
+ "IDScoreSwitcher",
"PeptideIndexer",
- "msconvert",
- "FalseDiscoveryRate",
"ConsensusID",
- "FidoAdapter",
- "PeakPickerHiRes",
- "IDPosteriorErrorProbability",
- "TextExporter",
"IDFilter",
+ "FalseDiscoveryRate",
"XTandemAdapter",
- "MSGFPlusAdapter",
+ "msconvert",
+ "FidoAdapter",
"FileInfo",
- "IDScoreSwitcher",
- "IDMerger"
+ "Grep1",
+ "TextExporter",
+ "PeakPickerHiRes",
+ "MSGFPlusAdapter",
+ "IDMerger",
+ "IDPosteriorErrorProbability"
],
"slides": false,
"slides_recordings": false,
@@ -631428,6 +584224,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -631483,10 +584283,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -631533,11 +584329,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -631582,6 +584373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -631634,10 +584429,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -631678,10 +584469,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -631724,6 +584511,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -631776,10 +584567,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -631818,8 +584605,8 @@
"state": "inexact",
"versions": [
"3.0.19052.0",
- "0.3.0",
- "3.0.20287.2"
+ "3.0.20287.2",
+ "0.3.0"
]
},
{
@@ -631827,11 +584614,6 @@
"state": "exact",
"version": "3.0.19052.1"
},
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- "version": "3.0.19052.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -631881,152 +584663,7 @@
"state": "missing"
},
{
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- "state": "missing"
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- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
@@ -632081,10 +584718,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "missing"
@@ -632131,9 +584764,150 @@
"version": "2.2.0"
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{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
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+ },
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+ "server": "https://usegalaxy.org",
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+ ],
+ "version": "2.2.0"
+ },
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+ "servers": [
+ {
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+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
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+ "server": "https://vm-chemflow-francegrille.eu/",
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "2.2.0"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.8+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.2.0"
+ },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632184,6 +584958,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -632236,10 +585014,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -632272,8 +585046,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.2.0",
- "2.1.0"
+ "2.1.0",
+ "2.2.0"
]
},
{
@@ -632288,10 +585062,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632342,6 +585112,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -632394,10 +585168,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -632443,10 +585213,6 @@
"state": "exact",
"version": "2.2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632493,6 +585259,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -632545,10 +585315,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -632596,10 +585362,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632646,6 +585408,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -632698,10 +585464,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -632747,10 +585509,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632797,6 +585555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -632849,10 +585611,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -632900,10 +585658,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -632950,6 +585704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633002,10 +585760,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633051,10 +585805,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633101,6 +585851,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633153,10 +585907,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633202,10 +585952,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633252,6 +585998,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633304,10 +586054,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633353,10 +586099,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633403,6 +586145,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633455,10 +586201,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633507,16 +586249,12 @@
"versions": [
"2.2.0",
"2.8+galaxy0",
- "2.5+galaxy0",
"2.3.0",
"2.6+galaxy0",
+ "2.5+galaxy0",
"3.1+galaxy0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633568,6 +586306,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633620,10 +586362,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633671,10 +586409,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633721,6 +586455,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633773,10 +586511,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633822,10 +586556,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -633872,6 +586602,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -633924,10 +586658,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -633975,10 +586705,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -634025,6 +586751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634077,10 +586807,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634126,10 +586852,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -634178,6 +586900,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634230,10 +586956,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634279,10 +587001,6 @@
"state": "exact",
"version": "2.3.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -634327,6 +587045,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634379,10 +587101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634428,10 +587146,6 @@
"state": "exact",
"version": "2.2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -634482,6 +587196,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634534,10 +587252,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634570,8 +587284,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.2.0",
- "2.1.0"
+ "2.1.0",
+ "2.2.0"
]
},
{
@@ -634586,10 +587300,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -634640,6 +587350,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634692,10 +587406,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634740,10 +587450,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -634790,6 +587496,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634842,10 +587552,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -634891,10 +587597,6 @@
"state": "exact",
"version": "2.2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -634941,6 +587643,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -634993,10 +587699,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -635044,10 +587746,6 @@
"state": "exact",
"version": "2.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -635125,7 +587823,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 178,
- "visitors": 2964,
+ "visitors": 2970,
"workflows": [
{
"creators": [],
@@ -635282,7 +587980,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nmzml input\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nfasta input\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"PeakPickerHiRes\"];\n 0 -->|output| 2;\n 3[\"XTandemAdapter\"];\n 1 -->|output| 3;\n 2 -->|param_out| 3;\n 4[\"FileInfo\"];\n 3 -->|out| 4;\n 5[\"PeptideIndexer\"];\n 1 -->|output| 5;\n 3 -->|out| 5;\n 6[\"IDPosteriorErrorProbability\"];\n 5 -->|out| 6;\n 7[\"FalseDiscoveryRate\"];\n 6 -->|out| 7;\n 8[\"IDScoreSwitcher\"];\n 7 -->|out| 8;\n 9[\"FileInfo\"];\n 8 -->|out| 9;\n 10[\"FidoAdapter\"];\n 8 -->|out| 10;\n 11[\"FalseDiscoveryRate\"];\n 10 -->|out| 11;\n 12[\"FileInfo\"];\n 11 -->|out| 12;\n 13[\"TextExporter\"];\n 11 -->|out| 13;\n 14[\"Select\"];\n 13 -->|out| 14;\n 15[\"Select\"];\n 13 -->|out| 15;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Proteomics: Peptide and Protein ID using OpenMS",
"outputs": [
{
@@ -636197,7 +588895,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Peptide And Protein ID Via OMS Using Two Search Engines",
"outputs": [
{
@@ -636802,8 +589500,8 @@
],
"dir": "topics/proteomics/tutorials/clinical-mp-5-data-interpretation",
"edam_operation": [
- "Prediction and recognition",
- "Visualisation"
+ "Visualisation",
+ "Prediction and recognition"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -636841,7 +589539,7 @@
"Analyze significant proteins",
"Look at the taxonomic distribution of the quantified peptides"
],
- "pageviews": 174,
+ "pageviews": 176,
"pub_date": "2024-02-06",
"questions": [
"Why do we need to interpret the data?",
@@ -636874,8 +589572,8 @@
],
"short_id": "T00417",
"short_tools": [
- "unipept",
"Grep1",
+ "unipept",
"msstatstmt"
],
"slides": false,
@@ -636928,6 +589626,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -636983,10 +589685,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -637033,11 +589731,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -637082,6 +589775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -637134,10 +589831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -637178,10 +589871,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -637224,6 +589913,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -637276,10 +589969,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -637322,10 +590011,6 @@
"state": "exact",
"version": "2.0.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -637370,6 +590055,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -637429,10 +590118,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -637479,10 +590164,6 @@
"state": "exact",
"version": "4.5.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -637540,8 +590221,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 421,
- "visitors": 130,
+ "visit_duration": 386,
+ "visitors": 132,
"workflows": [
{
"creators": [
@@ -637714,7 +590395,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nQuantified Peptides\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMaxQuant Protein Groups\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nMaxQuant Evidence\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nAnnotation.txt\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nComparison Matrix\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"Unipept\"];\n 0 -->|output| 5;\n 6[\"Microbial Proteins\"];\n 1 -->|output| 6;\n 7[\"Select\"];\n 1 -->|output| 7;\n 8[\"MSstatsTMT\"];\n 4 -->|output| 8;\n 3 -->|output| 8;\n 2 -->|output| 8;\n 6 -->|out_file1| 8;\n 9[\"HUMAN-Proteins\"];\n 7 -->|out_file1| 9;\n 10[\"MSstatsTMT\"];\n 4 -->|output| 10;\n 3 -->|output| 10;\n 2 -->|output| 10;\n 9 -->|out_file1| 10;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "WF5_Data_Interpretation_Worklow",
"outputs": [],
"parent_id": "proteomics/clinical-mp-5-data-interpretation",
@@ -637796,24 +590477,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n owner: galaxyp\n revisions: 7c45aa1c9464\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n owner: galaxyp\n revisions: eb65ab160a10\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n owner: galaxyp\n revisions: 7d1c20b315ff\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n owner: galaxyp\n revisions: 49a957fb353a\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n owner: galaxyp\n revisions: 982a442a98dd\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n owner: galaxyp\n revisions: 02da24eac445\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json",
- "contributions": {
- "authorship": [
- "subinamehta",
- "timothygriffin",
- "pratikdjagtap",
- "emmaleith",
- "mariecrane",
- "pravs3683"
- ],
- "reviewing": [
- "shiltemann",
- "bebatut",
- "subinamehta",
- "malloryfreeberg",
- "bgruening",
- "foellmelanie"
- ]
- },
"contributors": [
{
"email": "subinamehta@gmail.com",
@@ -637869,130 +590532,6 @@
"name": "Praveen Kumar",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "id": "subinamehta",
- "joined": "2018-06",
- "linkedin": "subinamehta",
- "matrix": "subinamehta:matrix.org",
- "name": "Subina Mehta",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
- "twitter": "Subina_Mehta",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
- },
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- "joined": "2017-09",
- "name": "Mallory Freeberg",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
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- "email": "melanie.foell@mol-med.uni-freiburg.de",
- "id": "foellmelanie",
- "joined": "2018-10",
- "matrix": "foellmelanie:matrix.org",
- "name": "Melanie F\u00f6ll",
- "orcid": "0000-0002-1887-7543",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
- "twitter": "MCFoell",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
}
],
"dir": "topics/proteomics/tutorials/metaquantome-taxonomy",
@@ -638005,16 +590544,16 @@
"topic_0637"
],
"edam_operation": [
- "Visualisation",
+ "Principal component visualisation",
+ "Filtering",
+ "Functional clustering",
"Heat map generation",
+ "Quantification",
"Differential protein expression analysis",
"Statistical inference",
+ "Visualisation",
"Indexing",
- "Quantification",
- "Filtering",
- "Query and retrieval",
- "Principal component visualisation",
- "Functional clustering"
+ "Query and retrieval"
],
"edam_topic": [
"Proteomics",
@@ -638062,7 +590601,7 @@
"objectives": [
"A taxonomy and quantitational analysis of metaproteomic mass spectrometry data."
],
- "pageviews": 527,
+ "pageviews": 529,
"pub_date": "2020-10-29",
"questions": [
"How do I look at differentially expressed taxa?",
@@ -638080,12 +590619,12 @@
],
"short_id": "T00224",
"short_tools": [
- "metaquantome_viz",
+ "metaquantome_filter",
"metaquantome_expand",
"metaquantome_db",
- "metaquantome_filter",
- "metaquantome_stat",
- "metaquantome_sample"
+ "metaquantome_viz",
+ "metaquantome_sample",
+ "metaquantome_stat"
],
"slides": false,
"slides_recordings": false,
@@ -638143,6 +590682,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -638198,10 +590741,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -638248,11 +590787,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -638297,6 +590831,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -638349,10 +590887,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -638398,10 +590932,6 @@
"state": "exact",
"version": "2.0.0-0"
},
- {
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -638453,6 +590983,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -638505,10 +591039,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -638554,10 +591084,6 @@
"state": "exact",
"version": "2.0.0-0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -638574,9 +591100,9 @@
"state": "inexact",
"versions": [
"2.0.2+galaxy0",
- "2.0.0-2",
+ "2.0.0-1",
"2.0.1+galaxy0",
- "2.0.0-1"
+ "2.0.0-2"
]
},
{
@@ -638609,6 +591135,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -638661,10 +591191,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -638710,10 +591236,6 @@
"state": "exact",
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},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -638765,6 +591287,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -638817,10 +591343,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -638866,10 +591388,6 @@
"state": "exact",
"version": "2.0.0-0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -638886,9 +591404,9 @@
"state": "inexact",
"versions": [
"2.0.2+galaxy0",
- "2.0.1+galaxy0",
+ "2.0.0-1",
"2.0.0-2",
- "2.0.0-1"
+ "2.0.1+galaxy0"
]
},
{
@@ -638921,6 +591439,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -638973,10 +591495,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -639022,10 +591540,6 @@
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -639042,8 +591556,8 @@
"state": "inexact",
"versions": [
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- "2.0.1+galaxy0",
"2.0.0-2",
+ "2.0.1+galaxy0",
"2.0.0-1"
]
},
@@ -639077,6 +591591,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -639129,10 +591647,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -639178,10 +591692,6 @@
"state": "exact",
"version": "2.0.0-0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -639199,8 +591709,8 @@
"versions": [
"2.0.2+galaxy0",
"2.0.0-2",
- "2.0.1+galaxy0",
- "2.0.0-1"
+ "2.0.0-1",
+ "2.0.1+galaxy0"
]
},
{
@@ -639246,7 +591756,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 158,
- "visitors": 394,
+ "visitors": 396,
"workflows": [
{
"creators": [],
@@ -639349,7 +591859,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"metaQuantome: create samples file\"];\n 1[\"\u2139\ufe0f Input Dataset\\nTaxa\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nIntensity\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"metaQuantome: database\"];\n 4[\"metaQuantome: expand\"];\n 3 -->|outfile| 4;\n 2 -->|output| 4;\n 1 -->|output| 4;\n 0 -->|samples_file| 4;\n 5[\"metaQuantome: filter\"];\n 4 -->|outfile| 5;\n 0 -->|samples_file| 5;\n 6[\"metaQuantome: stat\"];\n 5 -->|outfile| 6;\n 0 -->|samples_file| 6;\n 7[\"T2-Bar-Plot\"];\n 6 -->|outfile| 7;\n 0 -->|samples_file| 7;\n 8[\"T7-T2_volcano-plot\"];\n 6 -->|outfile| 8;\n 0 -->|samples_file| 8;\n 9[\"T4-Bar-Plot\"];\n 6 -->|outfile| 9;\n 0 -->|samples_file| 9;\n 10[\"T7-Bar-Plot\"];\n 6 -->|outfile| 10;\n 0 -->|samples_file| 10;\n 11[\"T4-T2_volcano-plot\"];\n 6 -->|outfile| 11;\n 0 -->|samples_file| 11;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "metaquantome-taxonomy-workflow",
"outputs": [
{
@@ -640028,20 +592538,6 @@
},
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@@ -640059,133 +592555,6 @@
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"twitter": "dblankenberg",
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- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "twitter": "Subina_Mehta",
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- "twitter": "MCFoell",
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}
],
"dir": "topics/proteomics/tutorials/peptide-library-data-analysis",
@@ -640211,20 +592580,20 @@
"Calculate descriptors",
"Quantitative analysis of peptide sequence properties"
],
- "pageviews": 846,
+ "pageviews": 852,
"pub_date": "2021-01-22",
"questions": [
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],
"short_id": "T00227",
"short_tools": [
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- "pdaug_merge_dataframes",
- "pdaug_addclasslabel",
- "pdaug_sequence_property_based_descriptors",
"pdaug_basic_plots",
+ "pdaug_sequence_property_based_descriptors",
"pdaug_peptide_sequence_analysis",
"pdaug_tsvtofasta",
+ "pdaug_merge_dataframes",
+ "pdaug_peptide_data_access",
+ "pdaug_addclasslabel",
"pdaug_fishers_plot"
],
"slides": false,
@@ -640262,6 +592631,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -640317,10 +592690,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -640367,11 +592736,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -640416,6 +592780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -640468,10 +592836,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -640513,10 +592877,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -640559,6 +592919,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -640611,10 +592975,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -640656,10 +593016,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -640702,6 +593058,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -640754,10 +593114,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -640799,10 +593155,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -640845,6 +593197,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -640897,10 +593253,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -640942,10 +593294,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -640988,6 +593336,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -641040,10 +593392,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -641085,10 +593433,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -641131,6 +593475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -641183,10 +593531,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -641228,10 +593572,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -641274,6 +593614,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -641326,10 +593670,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -641371,10 +593711,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -641417,6 +593753,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -641469,10 +593809,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -641514,10 +593850,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -641573,7 +593905,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 155,
- "visitors": 612,
+ "visitors": 616,
"workflows": [
{
"creators": [],
@@ -641597,7 +593929,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"PDAUG Peptide Data Access\"];\n 1[\"PDAUG TSVtoFASTA\"];\n 0 -->|output1| 1;\n 2[\"PDAUG Peptide Sequence Analysis\"];\n 1 -->|output3| 2;\n 1 -->|output2| 2;\n 3[\"PDAUG Sequence Property Based Descriptors\"];\n 1 -->|output2| 3;\n 4[\"PDAUG Sequence Property Based Descriptors\"];\n 1 -->|output3| 4;\n 5[\"PDAUG Fisher\u2019s Plot\"];\n 1 -->|output3| 5;\n 1 -->|output2| 5;\n 6[\"AMP\"];\n 3 -->|output1| 6;\n 7[\"TMP\"];\n 4 -->|output1| 7;\n 8[\"PDAUG Merge Dataframes\"];\n 6 -->|OutFile1| 8;\n 7 -->|OutFile1| 8;\n 9[\"PDAUG Basic Plots\"];\n 8 -->|output1| 9;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Copy of PeptideDataAnalysis (imported from uploaded file)",
"outputs": [
{
@@ -641829,21 +594161,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: proteore_clusterprofiler\n owner: proteore\n revisions: 2f67202ffdb3\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_expression_rnaseq_abbased\n owner: proteore\n revisions: dbeabf9bf091\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_filter_keywords_values\n owner: proteore\n revisions: b4641c0f8a82\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_id_converter\n owner: proteore\n revisions: 1e45ea50f145\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n owner: proteore\n revisions: 9cc475dcd0f2\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n owner: proteore\n revisions: 6c95f1b88627\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_tissue_specific_expression_data\n owner: proteore\n revisions: 3e65e0249976\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_venn_diagram\n owner: proteore\n revisions: 98b7912a9ceb\n tool_panel_section_label: Proteomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json",
- "contributions": {
- "authorship": [
- "vloux",
- "combesf",
- "davidchristiany",
- "yvandenb"
- ],
- "reviewing": [
- "shiltemann",
- "bebatut",
- "combesf",
- "foellmelanie",
- "bgruening"
- ]
- },
"contributors": [
{
"id": "vloux",
@@ -641877,122 +594194,6 @@
"name": "Yves Vandenbrouck",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvandenb/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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@@ -643561,7 +595687,7 @@
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"name": "'Proteome Annotation'",
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+ "state": "missing"
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@@ -645564,14 +597069,9 @@
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{
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{
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{
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{
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{
"server": "https://usegalaxy.org.au",
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{
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{
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@@ -645668,6 +597157,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -645698,7 +597191,12 @@
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{
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+ "1.0.0"
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{
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@@ -645720,14 +597218,10 @@
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@@ -645755,48 +597249,49 @@
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+ "state": "inexact",
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+ "1.0.0"
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{
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{
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+ "state": "inexact",
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+ ]
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{
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@@ -645818,6 +597313,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
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@@ -645840,20 +597339,15 @@
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@@ -645875,16 +597369,10 @@
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@@ -645913,47 +597401,42 @@
{
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{
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{
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@@ -645975,6 +597458,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -645997,21 +597484,20 @@
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+ "state": "inexact",
+ "versions": [
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+ ]
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{
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- "0.3.3"
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+ "state": "exact",
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{
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@@ -646033,15 +597519,11 @@
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{
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+ "1.0.2+galaxy2"
]
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{
@@ -646062,71 +597544,51 @@
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+ "state": "missing"
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{
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- "versions": [
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+ "state": "missing"
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{
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- "2.14.1+galaxy2",
- "0.3.3",
- "0.3.0",
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- "0.1.07"
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+ "state": "exact",
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{
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+ "version": "1.0.2+galaxy0"
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{
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+ "version": "1.0.2+galaxy0"
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{
"server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "2.10.1+galaxy0"
- ]
+ "state": "exact",
+ "version": "1.0.2+galaxy0"
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{
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+ "version": "1.0.2+galaxy0"
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{
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+ "version": "1.0.2+galaxy0"
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{
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},
{
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@@ -646148,6 +597610,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -646171,7 +597637,7 @@
{
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+ "version": "2.10.1+galaxy2"
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{
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@@ -646179,8 +597645,12 @@
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{
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+ "state": "inexact",
+ "versions": [
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+ "0.3.3",
+ "2.10.1+galaxy1"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -646202,14 +597672,12 @@
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- },
{
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- "version": "1.1.1"
+ "state": "inexact",
+ "versions": [
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+ ]
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{
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@@ -646229,56 +597697,66 @@
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{
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- "state": "missing"
+ "state": "inexact",
+ "versions": [
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+ ]
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "2.10.1+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.1.1"
+ "state": "inexact",
+ "versions": [
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+ "2.14.1+galaxy2",
+ "0.3.3",
+ "0.1.07",
+ "0.0.11",
+ "0.3.0"
+ ]
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{
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+ "version": "2.10.1+galaxy2"
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{
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- "version": "1.1.1"
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+ "version": "2.10.1+galaxy2"
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{
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- "state": "exact",
- "version": "1.1.1"
+ "state": "inexact",
+ "versions": [
+ "2.10.1+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.org",
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+ "version": "2.10.1+galaxy2"
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{
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+ "version": "2.10.1+galaxy2"
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{
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}
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+ "version": "2.10.1+galaxy2"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
"servers": [
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@@ -646300,6 +597778,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -646322,7 +597804,8 @@
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{
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+ "state": "exact",
+ "version": "1.1.1"
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{
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@@ -646330,7 +597813,8 @@
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{
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+ "state": "exact",
+ "version": "1.1.1"
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{
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@@ -646352,13 +597836,10 @@
"server": "http://galaxy.interactomix.com/",
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- },
{
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{
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@@ -646386,20 +597867,159 @@
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{
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{
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+ "version": "1.1.1"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "1.1.1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.1.1"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.1.1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.1.1"
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+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
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{
@@ -649099,7 +600669,7 @@
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Training Sanger sequences CHD8",
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{
@@ -649282,27 +600852,6 @@
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@@ -649371,226 +600920,6 @@
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- "uni-freiburg",
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- "twitter": "bebatut",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
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- "joined": "2017-09",
- "name": "Ekaterina Polkh",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/polkhe.json"
- },
- {
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- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
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- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
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- "name": "Maria Doyle",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/sequence-analysis/tutorials/mapping",
@@ -649598,17 +600927,17 @@
"topic_0102"
],
"edam_operation": [
- "Data handling",
+ "Validation",
+ "Sequence trimming",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
+ "Sequence composition calculation",
+ "Data handling",
"Sequence alignment analysis",
"Primer removal",
- "Validation",
- "Sequence trimming",
- "Sequence composition calculation",
"Read mapping",
- "Genome visualisation"
+ "Genome visualisation",
+ "Read pre-processing"
],
"edam_topic": [
"Mapping"
@@ -649643,7 +600972,6 @@
"GalaxyTrakr",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no"
],
"js_requirements": {
@@ -649664,7 +600992,7 @@
"Explain what is a BAM file and what it contains",
"Use genome browser to understand your data"
],
- "pageviews": 6277757,
+ "pageviews": 6300840,
"pub_date": "2016-10-04",
"questions": [
"What is mapping?",
@@ -649710,12 +601038,12 @@
"short_id": "T00237",
"short_tools": [
"fastqc",
- "bamFilter",
- "bowtie2",
"multiqc",
+ "samtools_stats",
+ "bamFilter",
"jbrowse",
"trim_galore",
- "samtools_stats"
+ "bowtie2"
],
"slides": true,
"slides_recordings": [
@@ -649772,11 +601100,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -649806,6 +601129,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -649861,10 +601188,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -649911,11 +601234,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -649960,6 +601278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650016,10 +601338,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -650063,14 +601381,6 @@
"state": "exact",
"version": "0.4.3.1"
},
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- "state": "inexact",
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- "0.6.7+galaxy0"
- ]
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -650116,6 +601426,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650172,10 +601486,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -650221,11 +601531,6 @@
"state": "exact",
"version": "2.4.1"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -650271,6 +601576,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650328,10 +601637,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -650380,11 +601685,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -650433,6 +601733,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650487,10 +601791,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -650532,12 +601832,12 @@
"state": "inexact",
"versions": [
"2.2.6",
- "2.2.6.2",
"2.3.2.2",
+ "2.2.6.2",
"0.2",
"0.4",
- "0.6",
"2.5.0+galaxy0",
+ "0.6",
"0.3"
]
},
@@ -650546,11 +601846,6 @@
"state": "exact",
"version": "2.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -650596,6 +601891,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650653,10 +601952,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -650707,9 +602002,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -650720,11 +602015,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -650770,6 +602060,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -650834,10 +602128,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -650886,16 +602176,6 @@
"state": "exact",
"version": "2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0.2+galaxy2",
- "2.0.4",
- "2.0.5",
- "2.0.3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -650945,6 +602225,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651005,10 +602289,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -651057,11 +602337,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -651107,6 +602382,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651167,10 +602446,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -651206,8 +602481,8 @@
"versions": [
"2.0.2+galaxy2",
"2.0",
- "2.0.1",
"2.0.2",
+ "2.0.1",
"2.0.2+galaxy1"
]
},
@@ -651223,11 +602498,6 @@
"state": "exact",
"version": "2.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -651277,6 +602547,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651340,10 +602614,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -651392,17 +602662,6 @@
"state": "exact",
"version": "1.16.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "1.16.11+galaxy1",
- "1.16.10+galaxy0",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -651452,6 +602711,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651515,10 +602778,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -651556,23 +602815,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -651587,17 +602846,6 @@
"state": "exact",
"version": "1.16.11+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "1.16.11+galaxy1",
- "1.16.10+galaxy0",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -651647,6 +602895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651672,9 +602924,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -651711,10 +602963,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -651764,11 +603012,6 @@
"state": "exact",
"version": "1.9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -651814,6 +603057,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -651839,9 +603086,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -651873,10 +603120,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -651929,11 +603172,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -651995,7 +603233,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 316,
- "visitors": 2299192,
+ "visitors": 2310106,
"workflows": [
{
"creators": [],
@@ -652112,7 +603350,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"];\n 0 -->|output| 2;\n 3[\"FastQC\"];\n 1 -->|output| 3;\n 4[\"Trim Galore!\"];\n 0 -->|output| 4;\n 1 -->|output| 4;\n 5[\"MultiQC\"];\n 3 -->|text_file| 5;\n 2 -->|text_file| 5;\n 6[\"Bowtie2\"];\n 4 -->|trimmed_reads_pair1| 6;\n 4 -->|trimmed_reads_pair2| 6;\n cb22563a-fece-4b63-9d85-ff5817edb5c3[\"Output\\nbowtie2_mapping_stats\"];\n 6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;\n style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;\n 7[\"Samtools stats\"];\n 6 -->|output| 7;\n 490620d4-f083-4999-bb33-73a2a1f736b4[\"Output\\nbam_stats_1\"];\n 7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;\n style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;\n 8[\"JBrowse\"];\n 6 -->|output| 8;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
"outputs": [
{
@@ -652481,7 +603719,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"];\n 0 -->|output| 2;\n 3[\"FastQC\"];\n 1 -->|output| 3;\n 4[\"Trim Galore!\"];\n 0 -->|output| 4;\n 1 -->|output| 4;\n 5[\"MultiQC\"];\n 3 -->|text_file| 5;\n 2 -->|text_file| 5;\n 6[\"Bowtie2\"];\n 4 -->|trimmed_reads_pair1| 6;\n 4 -->|trimmed_reads_pair2| 6;\n d2674912-28a6-45f3-ac48-6635eabe47b7[\"Output\\nbowtie2_mapping_stats\"];\n 6 --> d2674912-28a6-45f3-ac48-6635eabe47b7;\n style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px;\n 7[\"Stats\"];\n 6 -->|output| 7;\n 96de3c0c-4d7e-423b-8e9b-9a12a011d726[\"Output\\nbam_stats_1\"];\n 7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726;\n style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px;\n 8[\"Filter\"];\n 6 -->|output| 8;\n 9[\"Stats\"];\n 8 -->|out_file1| 9;\n 9603a94a-dcd8-4c1f-89cd-bb31d8572783[\"Output\\nbam_stats_2\"];\n 9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783;\n style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
"outputs": [
{
@@ -654989,15 +606227,15 @@
],
"dir": "topics/sequence-analysis/tutorials/quality-control",
"edam_operation": [
- "Scatter plot plotting",
+ "Validation",
+ "Sequence trimming",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Primer removal",
- "Box-Whisker plot plotting",
- "Validation",
"Sequence composition calculation",
- "Sequence trimming"
+ "Primer removal",
+ "Scatter plot plotting",
+ "Read pre-processing",
+ "Box-Whisker plot plotting"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -655020,8 +606258,7 @@
"id": "sequence-analysis/quality-control",
"inexact_supported_servers": [
"Galaxy@AuBi",
- "UseGalaxy.cz",
- "UseGalaxy.fr"
+ "UseGalaxy.cz"
],
"js_requirements": {
"mathjax": 23575,
@@ -655045,7 +606282,7 @@
"Summarise quality metrics MultiQC",
"Process single-end and paired-end data"
],
- "pageviews": 6347748,
+ "pageviews": 6370929,
"pub_date": "2016-10-04",
"questions": [
"How to perform quality control of NGS raw data?",
@@ -655094,12 +606331,12 @@
],
"short_id": "T00239",
"short_tools": [
- "fastqc",
"pycoqc",
- "cutadapt",
- "nanoplot",
"multiqc",
- "fastqe"
+ "fastqc",
+ "nanoplot",
+ "fastqe",
+ "cutadapt"
],
"slides": true,
"slides_recordings": [
@@ -655147,11 +606384,6 @@
"name": "UseGalaxy.cz",
"url": "https://usegalaxy.cz/",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -655177,6 +606409,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -655232,10 +606468,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -655282,11 +606514,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -655331,6 +606558,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -655388,10 +606619,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -655442,9 +606669,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -655455,11 +606682,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -655505,6 +606727,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -655562,10 +606788,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -655591,8 +606813,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -655616,12 +606838,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -655631,9 +606853,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -655644,11 +606866,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -655694,6 +606911,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -655752,10 +606973,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -655801,11 +607018,6 @@
"state": "exact",
"version": "0.2.6+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.2.6+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -655851,6 +607063,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -655876,9 +607092,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -655910,10 +607126,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -655966,11 +607178,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -656016,6 +607223,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -656077,10 +607288,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -656132,11 +607339,6 @@
"state": "exact",
"version": "1.41.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.41.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -656186,6 +607388,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -656241,10 +607447,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -656287,11 +607489,6 @@
"state": "exact",
"version": "2.5.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.5.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -656336,6 +607533,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -656375,8 +607576,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -656399,10 +607600,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -656455,31 +607652,6 @@
"state": "exact",
"version": "1.16.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.0+galaxy0",
- "4.8+galaxy1",
- "4.9+galaxy1",
- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
- "3.5+galaxy0",
- "3.4+galaxy2",
- "4.6+galaxy0",
- "3.4+galaxy1",
- "4.6+galaxy1",
- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -656527,6 +607699,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -656566,8 +607742,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -656590,10 +607766,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -656636,8 +607808,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -656652,11 +607824,6 @@
"state": "exact",
"version": "3.4+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.4+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -656704,6 +607871,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -656741,8 +607912,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -656765,10 +607936,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -656811,8 +607978,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -656827,11 +607994,6 @@
"state": "exact",
"version": "4.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -656891,8 +608053,8 @@
"video": true,
"video_versions": 3,
"video_view": 0,
- "visit_duration": 336,
- "visitors": 2331361,
+ "visit_duration": 335,
+ "visitors": 2342375,
"workflows": [
{
"creators": [],
@@ -657016,7 +608178,7 @@
],
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"name": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
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},
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@@ -658730,16 +609806,15 @@
],
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"Data handling",
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"Read mapping",
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],
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@@ -658775,7 +609850,7 @@
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],
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+ "pageviews": 4998,
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"questions": [
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@@ -658799,24 +609874,19 @@
],
"short_id": "T00236",
"short_tools": [
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+ "bwa_mem",
+ "trimmomatic",
"__UNZIP_COLLECTION__",
+ "Grep1",
+ "seqtk_subseq",
"samtools_fastx",
"tp_replace_in_line",
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"url": "https://usegalaxy.org",
@@ -658888,6 +609958,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://mississippi.sorbonne-universite.fr",
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"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -659042,6 +610107,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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{
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"state": "local"
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"state": "local"
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"state": "local"
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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"state": "exact",
@@ -659783,6 +610826,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
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"state": "missing"
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"state": "exact",
@@ -659941,6 +610979,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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"state": "missing"
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{
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"state": "exact",
@@ -660096,6 +611129,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"state": "missing"
@@ -660129,8 +611166,8 @@
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+ "0.38.1",
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"state": "inexact",
@@ -660205,31 +611238,26 @@
"0.38.1",
"0.36.4",
"0.32.3",
+ "0.36.0",
"0.32.1",
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+ "0.32.2"
]
},
{
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"state": "inexact",
"versions": [
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"0.39+galaxy0",
+ "0.38.1",
"0.36.4",
"0.39+galaxy2",
"0.36.5",
"0.32.3",
+ "0.36.0",
"0.32.1",
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{
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"state": "inexact",
@@ -660282,6 +611310,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
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{
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{
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@@ -660379,8 +611407,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
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"0.36.6",
+ "0.38.0",
"0.39+galaxy2",
"0.36.5",
"0.32.3"
@@ -660396,11 +611424,6 @@
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},
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- "version": "0.38.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -660465,7 +611488,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 139,
- "visitors": 3554,
+ "visitors": 3559,
"workflows": [
{
"creators": [],
@@ -660535,7 +611558,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
"outputs": [
{
@@ -661242,9 +612265,9 @@
],
"dir": "topics/sequence-analysis/tutorials/ncbi-fcs",
"edam_operation": [
- "Sequence trimming",
+ "Sequence assembly validation",
"Sequence contamination filtering",
- "Sequence assembly validation"
+ "Sequence trimming"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -661271,15 +612294,15 @@
"Learn how to screen a genome assembly for adaptor and vector contamination.",
"Learn how to screen a genome assembly for non-host organism contamination."
],
- "pageviews": 879,
+ "pageviews": 892,
"pub_date": "2024-04-16",
"questions": [
"Are the sequences in a genome assembly contaminant-free?"
],
"short_id": "T00439",
"short_tools": [
- "ncbi_fcs_adaptor",
- "ncbi_fcs_gx"
+ "ncbi_fcs_gx",
+ "ncbi_fcs_adaptor"
],
"slides": false,
"slides_recordings": false,
@@ -661320,6 +612343,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -661375,10 +612402,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -661425,11 +612448,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -661474,6 +612492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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"state": "missing"
@@ -661527,10 +612549,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -661572,10 +612590,6 @@
"state": "exact",
"version": "0.5.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -661619,6 +612633,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -661672,10 +612690,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -661716,10 +612730,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -661768,8 +612778,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 146,
- "visitors": 636,
+ "visit_duration": 144,
+ "visitors": 646,
"workflows": [
{
"creators": [
@@ -661834,7 +612844,7 @@
],
"license": "http://www.usa.gov/publicdomain/label/1.0/",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nInput genome\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"FCS-GX screen\"];\n 0 -->|output| 1;\n 9741edf2-4be6-45a3-980d-99b1aea18380[\"Output\\nfcs_gx_action_report\"];\n 1 --> 9741edf2-4be6-45a3-980d-99b1aea18380;\n style 9741edf2-4be6-45a3-980d-99b1aea18380 stroke:#2c3143,stroke-width:4px;\n ddedd49f-8c57-4e3e-a158-3d66ce12f05c[\"Output\\nfcs_gx_taxonomy_report\"];\n 1 --> ddedd49f-8c57-4e3e-a158-3d66ce12f05c;\n style ddedd49f-8c57-4e3e-a158-3d66ce12f05c stroke:#2c3143,stroke-width:4px;\n 2[\"FCS-GX clean\"];\n 1 -->|action_report| 2;\n 0 -->|output| 2;\n f3a37b43-d304-4ec0-a023-197c9e0ce2e1[\"Output\\ngx_contam_fasta\"];\n 2 --> f3a37b43-d304-4ec0-a023-197c9e0ce2e1;\n style f3a37b43-d304-4ec0-a023-197c9e0ce2e1 stroke:#2c3143,stroke-width:4px;\n 56716c7c-ac7f-42f7-bbef-62a36b4d3810[\"Output\\ngx_clean_fasta\"];\n 2 --> 56716c7c-ac7f-42f7-bbef-62a36b4d3810;\n style 56716c7c-ac7f-42f7-bbef-62a36b4d3810 stroke:#2c3143,stroke-width:4px;\n 3[\"FCS-adaptor screen\"];\n 2 -->|clean_fasta| 3;\n 6a4baf46-80b0-4a96-b864-9201fc80cdb7[\"Output\\nfcs_adaptor_report\"];\n 3 --> 6a4baf46-80b0-4a96-b864-9201fc80cdb7;\n style 6a4baf46-80b0-4a96-b864-9201fc80cdb7 stroke:#2c3143,stroke-width:4px;\n 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb[\"Output\\nadaptor_clean_fasta\"];\n 3 --> 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb;\n style 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb stroke:#2c3143,stroke-width:4px;\n 4[\"FCS-adaptor clean\"];\n 3 -->|adaptor_report| 4;\n 2 -->|clean_fasta| 4;\n 0da68570-7490-4087-86c8-739522e1a776[\"Output\\nadaptor_contam_fasta\"];\n 4 --> 0da68570-7490-4087-86c8-739522e1a776;\n style 0da68570-7490-4087-86c8-739522e1a776 stroke:#2c3143,stroke-width:4px;\n 4985eb07-30b0-4872-ab83-52ffeb619900[\"Output\\nfinal_clean_fasta\"];\n 4 --> 4985eb07-30b0-4872-ab83-52ffeb619900;\n style 4985eb07-30b0-4872-ab83-52ffeb619900 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "NCBI Foreign Contamination Screen",
"outputs": [
{
@@ -662371,13 +613381,13 @@
"topic_3697"
],
"edam_operation": [
+ "Sequencing quality control",
"Sequence composition calculation",
+ "Taxonomic classification",
+ "Sequence contamination filtering",
"Expression analysis",
- "Statistical calculation",
- "Sequencing quality control",
"Cross-assembly",
- "Taxonomic classification",
- "Sequence contamination filtering"
+ "Statistical calculation"
],
"edam_topic": [
"Whole genome sequencing",
@@ -662386,8 +613396,7 @@
"Microbial ecology"
],
"exact_supported_servers": [
- "UseGalaxy.eu",
- "UseGalaxy.fr"
+ "UseGalaxy.eu"
],
"feedback_mean_note": null,
"feedback_number": 0,
@@ -662421,7 +613430,7 @@
"Run a series of tool to identify species in bacterial isolate sequencing data",
"Visualize the species abundance"
],
- "pageviews": 680,
+ "pageviews": 707,
"pub_date": "2024-07-15",
"questions": [
"How to check the quality of MiSeq data?",
@@ -662444,12 +613453,12 @@
],
"short_id": "T00446",
"short_tools": [
- "fastqc",
- "upload1",
+ "kraken2",
"est_abundance",
"fastp",
+ "fastqc",
"recentrifuge",
- "kraken2"
+ "upload1"
],
"slides": false,
"slides_recordings": false,
@@ -662459,11 +613468,6 @@
"name": "UseGalaxy.eu",
"url": "https://usegalaxy.eu",
"usegalaxy": true
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
],
"inexact": [
@@ -662511,6 +613515,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -662566,10 +613574,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -662616,11 +613620,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -662665,6 +613664,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -662690,8 +613693,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -662728,10 +613731,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -662755,8 +613754,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -662776,12 +613775,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -662794,11 +613793,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -662847,6 +613841,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -662882,8 +613880,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.5+galaxy0",
- "2.6.1+galaxy0"
+ "2.6.1+galaxy0",
+ "2.5+galaxy0"
]
},
{
@@ -662906,10 +613904,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -662952,11 +613946,6 @@
"state": "exact",
"version": "2.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -663011,6 +614000,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -663046,8 +614039,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.5+galaxy0",
- "2.6.1+galaxy0"
+ "2.6.1+galaxy0",
+ "2.5+galaxy0"
]
},
{
@@ -663070,10 +614063,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -663118,11 +614107,6 @@
"state": "exact",
"version": "2.9+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.9+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -663171,6 +614155,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -663226,10 +614214,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -663267,198 +614251,188 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
- "0.19.3.2",
- "0.19.5"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
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- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.23.2+galaxy0"
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
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- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
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- {
- "server": "https://usegalaxy.org",
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- {
- "server": "https://usegalaxy.org.au",
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- "version": "0.23.2+galaxy0"
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- {
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- "version": "0.23.2+galaxy0"
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"0.19.3.2",
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]
},
{
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+ "state": "missing"
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+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+ },
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+ "server": "https://galaxy.mesocentre.uca.fr",
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]
},
{
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+ "server": "https://galaxy.pasteur.fr/",
+ "state": "inexact",
+ "versions": [
+ "0.23.2+galaxy0"
+ ]
+ },
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+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
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+ "0.23.2+galaxy0"
+ ]
+ },
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+ "server": "http://hyperbrowser.uio.no/hb/",
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+ "server": "http://gigagalaxy.net/",
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+ "server": "https://www.immportgalaxy.org/",
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+ "server": "http://galaxy.interactomix.com/",
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},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
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+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.20.1+galaxy0",
+ "0.19.5+galaxy1",
+ "0.19.3.2",
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "0.23.2+galaxy0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.23.4+galaxy0"
},
@@ -663478,9 +614452,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -663521,6 +614495,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -663575,10 +614553,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -663612,8 +614586,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -663626,11 +614600,6 @@
"state": "exact",
"version": "2.1.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -663676,6 +614645,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -663730,10 +614703,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -663769,8 +614738,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -663785,11 +614754,6 @@
"state": "exact",
"version": "2.1.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -663839,6 +614803,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -663897,10 +614865,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -663943,11 +614907,6 @@
"state": "exact",
"version": "1.12.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.12.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -663957,8 +614916,8 @@
"state": "inexact",
"versions": [
"1.14.1+galaxy0",
- "1.14.0+galaxy0",
- "1.15.0+galaxy0"
+ "1.15.0+galaxy0",
+ "1.14.0+galaxy0"
]
},
{
@@ -663999,6 +614958,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -664051,10 +615014,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -664095,10 +615054,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -664158,8 +615113,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 286,
- "visitors": 521,
+ "visit_duration": 288,
+ "visitors": 538,
"workflows": [
{
"creators": [
@@ -664251,7 +615206,7 @@
],
"license": "GPL-3.0-or-later",
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- "modified": "2024-12-09 08:53:35 +0000",
+ "modified": "2024-12-13 13:26:18 +0000",
"name": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
"outputs": [
{
@@ -664825,6 +615780,9 @@
},
{
"avatar": "/training-material/shared/images/logo-dataplant.svg",
+ "funder_name": "DFG",
+ "funding_database": "dfg",
+ "funding_id": "442077441",
"id": "nfdi4plants",
"joined": "2024-07",
"members": [
@@ -664839,7 +615797,7 @@
"name": "DataPLANT (NFDI4Plants)",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
"short_name": "DataPLANT",
- "url": "https://training.galaxyproject.org/training-material/api/organisations/nfdi4plants.json"
+ "url": "https://training.galaxyproject.org/training-material/api/grants/nfdi4plants.json"
},
{
"affiliations": [
@@ -664967,7 +615925,6 @@
"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -664996,7 +615953,7 @@
"Load FASTA sequence into Galaxy",
"Perform NCBI-Blast+ analysis against MAdLandDB"
],
- "pageviews": 1553,
+ "pageviews": 1556,
"pub_date": "2023-01-16",
"questions": [
"What is MAdLand DB?",
@@ -665005,8 +615962,8 @@
"short_id": "T00238",
"short_tools": [
"ncbi_blastp_wrapper",
- "ncbi_blastx_wrapper",
- "bg_diamond"
+ "bg_diamond",
+ "ncbi_blastx_wrapper"
],
"slides": false,
"slides_recordings": false,
@@ -665022,11 +615979,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -665078,6 +616030,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -665133,10 +616089,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -665183,11 +616135,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -665232,6 +616179,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -665291,10 +616242,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -665337,11 +616284,6 @@
"state": "exact",
"version": "2.0.15+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.15+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -665387,6 +616329,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -665421,8 +616367,8 @@
"state": "inexact",
"versions": [
"2.10.1+galaxy1",
- "2.14.1+galaxy2",
- "0.3.3"
+ "0.3.3",
+ "2.14.1+galaxy2"
]
},
{
@@ -665445,10 +616391,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -665491,8 +616433,8 @@
"state": "inexact",
"versions": [
"0.3.1",
- "2.14.1+galaxy2",
"0.3.3",
+ "2.14.1+galaxy2",
"0.0.11",
"0.1.07",
"0.3.0"
@@ -665508,11 +616450,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -665560,6 +616497,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -665593,9 +616534,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.3.3",
+ "2.10.1+galaxy1",
"2.14.1+galaxy2",
- "2.10.1+galaxy1"
+ "0.3.3"
]
},
{
@@ -665618,10 +616559,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -665664,10 +616601,10 @@
"state": "inexact",
"versions": [
"0.3.1",
- "0.3.3",
"2.14.1+galaxy2",
- "0.3.0",
+ "0.3.3",
"0.1.07",
+ "0.3.0",
"0.0.11"
]
},
@@ -665681,11 +616618,6 @@
"state": "exact",
"version": "2.10.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.10.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -665743,7 +616675,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 162,
- "visitors": 1218,
+ "visitors": 1220,
"zenodo_link": "https://zenodo.org/records/7524427"
},
{
@@ -666000,19 +616932,18 @@
],
"dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
"edam_operation": [
+ "Sequence alignment",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
"Sequence composition calculation",
- "Read mapping",
"Generation",
+ "Read mapping",
"Genome visualisation",
"Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -666046,7 +616977,7 @@
"Critique large data sets and use bioinformatics to assess genetics data",
"Tap into the interdisciplinary nature of science"
],
- "pageviews": 1043,
+ "pageviews": 1050,
"pub_date": "2023-07-10",
"questions": [
"How do I check my data quality?",
@@ -666055,8 +616986,8 @@
],
"short_id": "T00356",
"short_tools": [
- "jbrowse",
"fastqc",
+ "jbrowse",
"bwa_mem"
],
"slides": false,
@@ -666068,11 +616999,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -666144,6 +617070,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -666199,10 +617129,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -666249,11 +617175,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -666298,6 +617219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -666357,10 +617282,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -666408,11 +617329,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -666459,6 +617375,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -666516,10 +617436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -666545,8 +617461,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
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"Sequence composition calculation",
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"fastqc",
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"anndata_inspect",
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"sinto_fragments",
+ "sinto_barcode",
"scanpy_plot",
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+ "episcanpy_build_matrix",
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{
"name": "CoralSNP",
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"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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@@ -668657,6 +619381,10 @@
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@@ -668752,8 +619476,8 @@
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"2.1.1.20160309.4",
"2.1.1.20160309.6",
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- "2.1.1.20160309.3"
+ "2.1.1.20160309.3",
+ "2.1.1.20160309.0"
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@@ -668766,11 +619490,6 @@
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- "state": "exact",
- "version": "2.2.7.1+galaxy0"
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"state": "exact",
@@ -668816,6 +619535,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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@@ -668904,10 +619623,10 @@
"server": "https://usegalaxy.be/",
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"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
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@@ -668923,10 +619642,6 @@
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- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -668975,6 +619690,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -669027,10 +619746,6 @@
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"server": "https://mississippi.sorbonne-universite.fr",
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@@ -669063,10 +619778,10 @@
"server": "https://usegalaxy.be/",
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"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -669080,10 +619795,6 @@
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"version": "1.7.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -669129,6 +619840,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -669181,10 +619896,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -669227,10 +619938,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -669275,6 +619982,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -669327,10 +620038,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -669373,10 +620080,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -669441,8 +620144,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 67,
- "visitors": 4219,
+ "visit_duration": 68,
+ "visitors": 4267,
"workflows": [
{
"creators": [
@@ -669500,7 +620203,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nscATAC-seq Anndata\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"scATAC-seq Preprocessing\"];\n 0 -->|output| 1;\n 2[\"scATAC-seq Preprocessing\"];\n 1 -->|anndata_out| 2;\n 3[\"scATAC-seq Preprocessing\"];\n 2 -->|anndata_out| 3;\n 4[\"Plot\"];\n 3 -->|anndata_out| 4;\n 5[\"scATAC-seq Preprocessing\"];\n 3 -->|anndata_out| 5;\n 6[\"scATAC-seq Preprocessing\"];\n 3 -->|anndata_out| 6;\n 7[\"scATAC-seq Preprocessing\"];\n 3 -->|anndata_out| 7;\n 8[\"scATAC-seq Preprocessing\"];\n 3 -->|anndata_out| 8;\n 9[\"scATAC-seq Preprocessing\"];\n 8 -->|anndata_out| 9;\n 10[\"scATAC-seq Preprocessing\"];\n 9 -->|anndata_out| 10;\n 11[\"scATAC-seq Preprocessing\"];\n 10 -->|anndata_out| 11;\n 12[\"Plot\"];\n 11 -->|anndata_out| 12;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "scATAC-seq Count Matrix Filtering",
"outputs": [],
"parent_id": "single-cell/scatac-preprocessing-tenx",
@@ -669634,7 +620337,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nForward reads FASTQ R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nBarcodes FASTQ R2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nReverse reads FASTQ R3\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Sinto barcode\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 2 -->|output| 3;\n 4[\"FastQC\"];\n 3 -->|read1_out| 4;\n 5[\"FastQC\"];\n 3 -->|read2_out| 5;\n 6[\"Map with BWA-MEM\"];\n 3 -->|read1_out| 6;\n 3 -->|read2_out| 6;\n 7[\"Sinto fragments\"];\n 6 -->|bam_output| 7;\n 8[\"bedtools SortBED\"];\n 7 -->|fragments| 8;\n 9[\"MACS2 callpeak\"];\n 8 -->|output| 9;\n 10[\"Unique\"];\n 9 -->|output_narrowpeaks| 10;\n 11[\"Build count matrix\"];\n 8 -->|output| 11;\n 10 -->|outfile| 11;\n 12[\"Inspect AnnData\"];\n 11 -->|anndata_out| 12;\n 13[\"Inspect AnnData\"];\n 11 -->|anndata_out| 13;\n 14[\"Inspect AnnData\"];\n 11 -->|anndata_out| 14;\n 15[\"Inspect AnnData\"];\n 11 -->|anndata_out| 15;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "scATAC-seq FASTQ to Count Matrix",
"outputs": [],
"parent_id": "single-cell/scatac-preprocessing-tenx",
@@ -669776,26 +620479,6 @@
},
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@@ -669845,251 +620528,41 @@
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+ "email": "anikaerxleben@gmail.com",
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},
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- "elixir_node": "fr",
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- "fediverse": "https://genomic.social/@abretaud",
+ "elixir_node": "de",
+ "fediverse": "https://scholar.social/@zerodivision",
"fediverse_flavor": "mastodon",
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],
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"edam_operation": [
- "Data handling",
"Sequencing quality control",
"RNA-Seq quantification",
- "Read summarisation",
+ "Validation",
+ "Data handling",
"Sequence alignment analysis",
"Sequence alignment",
- "Validation"
+ "Read summarisation"
],
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@@ -670112,7 +620585,6 @@
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- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -670136,7 +620608,7 @@
"Obtain an overview of general alignment and quantification techniques",
"Generate a count matrix for downstream single-cell RNA analysis"
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"priority": 1,
"pub_date": "2019-02-22",
"questions": [
@@ -670162,16 +620634,16 @@
],
"short_id": "T00251",
"short_tools": [
- "bamFilter",
- "collection_column_join",
- "multiqc",
+ "tp_sed_tool",
"featurecounts",
- "__FLATTEN__",
+ "multiqc",
+ "umi_tools_count",
+ "rna_star",
"umi_tools_extract",
+ "bamFilter",
+ "collection_column_join",
"samtools_stats",
- "tp_sed_tool",
- "umi_tools_count",
- "rna_star"
+ "__FLATTEN__"
],
"slides": true,
"slides_recordings": false,
@@ -670195,11 +620667,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -670239,6 +620706,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -670294,10 +620765,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -670344,11 +620811,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -670393,6 +620855,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -670445,10 +620911,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -670489,10 +620951,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -670535,6 +620993,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -670589,10 +621051,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -670639,11 +621097,6 @@
"state": "exact",
"version": "1.1.1"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -670689,6 +621142,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -670745,10 +621202,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -670794,11 +621247,6 @@
"state": "exact",
"version": "2.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -670844,6 +621292,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -670908,10 +621360,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -670946,209 +621394,48 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "2.0.1"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "2.0.1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0.2+galaxy2",
- "2.0.4",
- "2.0.5",
- "2.0.3"
- ]
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "2.0.2+galaxy2",
- "2.0.4",
- "2.0.3"
- ]
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "2.0.1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.0.1"
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- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
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- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
- },
- {
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
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- "state": "missing"
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- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
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- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "0.0.3"
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- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
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- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
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- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "0.0.3"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
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- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "0.0.3"
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "0.0.3"
+ "state": "inexact",
+ "versions": [
+ "2.0.4"
+ ]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "0.0.3"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.0.3"
+ "state": "inexact",
+ "versions": [
+ "2.0.2+galaxy2",
+ "2.0.4",
+ "2.0.3"
+ ]
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "0.0.3"
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "0.0.3"
+ "version": "2.0.1"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
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+ "version": "2.0.1"
},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -671170,6 +621457,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -671192,12 +621483,7 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "inexact",
- "versions": [
- "2.0.3+galaxy2",
- "1.6.4+galaxy1",
- "1.6.3"
- ]
+ "state": "missing"
},
{
"server": "https://galaxy.pasteur.fr/",
@@ -671205,11 +621491,8 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
- "1.6.4+galaxy1",
- "2.0.1"
- ]
+ "state": "exact",
+ "version": "0.0.3"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -671231,16 +621514,10 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
- "2.0.3+galaxy2"
- ]
+ "state": "exact",
+ "version": "0.0.3"
},
{
"server": "https://neo.engr.uconn.edu/",
@@ -671264,73 +621541,47 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "inexact",
- "versions": [
- "2.0.1"
- ]
+ "state": "missing"
},
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "1.6.2"
+ "version": "0.0.3"
},
{
"server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2.0.3+galaxy2",
- "2.0.3+galaxy1"
- ]
+ "state": "exact",
+ "version": "0.0.3"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.6.2"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "1.6.4+galaxy1",
- "2.0.1",
- "2.0.3+galaxy1",
- "2.0.6+galaxy0",
- "2.0.1+galaxy1",
- "2.0.3+galaxy0",
- "1.6.4+galaxy2",
- "2.0.1+galaxy2"
- ]
+ "version": "0.0.3"
},
{
"server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "2.0.1",
- "2.0.1+galaxy1",
- "1.6.4+galaxy2",
- "2.0.1+galaxy2"
- ]
+ "state": "exact",
+ "version": "0.0.3"
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "1.6.2"
+ "version": "0.0.3"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "1.6.2"
+ "version": "0.0.3"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.6.2"
+ "version": "0.0.3"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -671352,6 +621603,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -671387,8 +621642,11 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "2.0.1"
+ "state": "inexact",
+ "versions": [
+ "1.6.4+galaxy1",
+ "2.0.1"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -671410,10 +621668,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -671443,21 +621697,16 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "exact",
- "version": "2.0.1"
- },
- {
- "server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.6.4+galaxy1",
- "1.6.3",
- "1.6.4",
- "1.6.3+galaxy2",
- "1.4.6.p5",
- "1.6.2"
+ "2.0.1"
]
},
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.6.2"
+ },
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
@@ -671469,37 +621718,37 @@
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "2.0.1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.1"
+ "version": "1.6.2"
},
{
"server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "2.0.1"
+ "state": "inexact",
+ "versions": [
+ "2.0.1",
+ "1.6.4+galaxy2",
+ "2.0.1+galaxy1",
+ "2.0.1+galaxy2"
+ ]
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "2.0.1"
+ "version": "1.6.2"
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "2.0.1"
+ "version": "1.6.2"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "2.0.1"
+ "version": "1.6.2"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -671521,6 +621770,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -671545,10 +621798,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.11+galaxy1",
- "1.11+galaxy0",
- "1.7",
- "1.6"
+ "2.0.3+galaxy2",
+ "1.6.4+galaxy1",
+ "1.6.3"
]
},
{
@@ -671557,13 +621809,8 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1",
- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1"
- ]
+ "state": "exact",
+ "version": "2.0.1"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -671585,15 +621832,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "1.11+galaxy1"
+ "2.0.3+galaxy2"
]
},
{
@@ -671618,99 +621861,58 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1"
- ]
+ "state": "exact",
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.9",
- "1.8+galaxy0"
+ "1.6.4+galaxy1",
+ "1.6.3",
+ "1.6.2",
+ "1.6.3+galaxy2",
+ "1.4.6.p5",
+ "1.6.4"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.11+galaxy1",
- "1.11+galaxy0",
- "1.7",
- "1.6",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.2.0",
- "1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "2.0.3+galaxy2",
+ "2.0.3+galaxy1"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.5.0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1",
- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy1",
- "1.24.1+galaxy0"
- ]
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
- ]
+ "state": "exact",
+ "version": "2.0.1"
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "1.5.0"
+ "version": "2.0.1"
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{
"server": "https://usegalaxy.org.au",
- "state": "inexact",
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- "1.6",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.7.1",
- "1.8+galaxy1",
- "1.24.1+galaxy0"
- ]
+ "state": "exact",
+ "version": "2.0.1"
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.5.0"
+ "version": "2.0.1"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -671732,6 +621934,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -671757,9 +621963,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -671796,10 +622002,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -671836,48 +622038,78 @@
},
{
"server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.9"
+ "state": "inexact",
+ "versions": [
+ "1.9",
+ "1.8+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.9"
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1",
+ "1.6",
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1",
+ "1.9",
+ "1.8+galaxy0",
+ "1.8+galaxy2",
+ "1.8+galaxy1",
+ "1.7.1",
+ "1.2.0"
+ ]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "1.9"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9"
+ "version": "1.5.0"
},
{
"server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "1.9"
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1",
+ "1.9",
+ "1.8+galaxy0",
+ "1.8+galaxy2",
+ "1.8+galaxy1",
+ "1.7.1"
+ ]
},
{
"server": "https://usegalaxy.org",
"state": "exact",
- "version": "1.9"
+ "version": "1.5.0"
},
{
"server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.9"
+ "state": "inexact",
+ "versions": [
+ "1.11+galaxy1",
+ "1.6",
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1",
+ "1.9",
+ "1.8+galaxy0",
+ "1.8+galaxy1",
+ "1.7.1",
+ "1.24.1+galaxy0"
+ ]
},
{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
- "version": "1.9"
+ "version": "1.5.0"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -671899,6 +622131,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -671923,23 +622159,24 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "1.11+galaxy1",
+ "1.6",
+ "1.11+galaxy0",
+ "1.7"
]
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "inexact",
- "versions": [
- "2.7.11a+galaxy1"
- ]
+ "state": "missing"
},
{
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.7.8a"
+ "1.11+galaxy1",
+ "1.11+galaxy0",
+ "1.7",
+ "1.9+galaxy1"
]
},
{
@@ -671962,15 +622199,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
"versions": [
- "2.7.11a+galaxy0"
+ "1.11+galaxy1"
]
},
{
@@ -671997,109 +622230,48 @@
"server": "https://galaxy.bio.di.uminho.pt/",
"state": "inexact",
"versions": [
- "2.7.8a+galaxy1"
+ "1.11+galaxy1"
]
},
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "2.5.2b-2"
+ "version": "1.9"
},
{
"server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
- ]
+ "state": "exact",
+ "version": "1.9"
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "2.5.2b-2"
- },
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- "server": "https://usegalaxy.fr/",
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- "2.7.2b",
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- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4",
- "2.7.10b+galaxy1",
- "2.7.6a",
- "2.7.10b+galaxy2",
- "2.7.10b+galaxy0"
- ]
+ "version": "1.9"
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{
"server": "https://usegalaxy.no/",
- "state": "inexact",
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- "2.7.8a",
- "2.7.5b",
- "2.7.7a",
- "2.7.10b+galaxy4",
- "2.7.6a"
- ]
+ "state": "exact",
+ "version": "1.9"
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{
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- "2.7.7a",
- "2.6.0b-1",
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
- ]
+ "state": "exact",
+ "version": "1.9"
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{
"server": "https://usegalaxy.org.au",
- "state": "inexact",
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- "2.7.2b",
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- "2.7.10b+galaxy1",
- "2.7.6a",
- "2.5.2b-1",
- "2.7.10b+galaxy2"
- ]
+ "state": "exact",
+ "version": "1.9"
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{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
],
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+ "version": "1.9"
},
{
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a",
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
"servers": [
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@@ -672121,6 +622293,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -672146,8 +622322,8 @@
"state": "inexact",
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- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -672184,10 +622360,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -672225,67 +622397,81 @@
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "2.7.7a"
+ "version": "2.5.2b-2"
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
- "version": "2.7.7a"
+ "version": "2.5.2b-2"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "2.7.8a+galaxy0",
+ "2.7.8a",
+ "2.7.5b",
+ "2.7.7a",
+ "2.7.10b+galaxy4",
+ "2.7.6a"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.11a+galaxy1",
"2.7.8a",
"2.7.8a+galaxy1",
- "2.6.0b-2",
"2.7.5b",
- "2.7.2a",
+ "2.7.7a",
+ "2.6.0b-1",
"2.5.2b-0",
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"2.7.10b+galaxy4",
- "2.7.10b+galaxy1",
- "2.7.6a",
- "2.7.10b+galaxy2",
- "2.7.10b+galaxy0"
+ "2.7.10b+galaxy3"
]
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- "version": "2.7.7a"
- },
{
"server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "2.7.7a"
+ "state": "inexact",
+ "versions": [
+ "2.7.8a+galaxy0",
+ "2.7.11a+galaxy0",
+ "2.7.2b",
+ "2.7.11a+galaxy1",
+ "2.7.8a",
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+ "2.7.5b",
+ "2.7.7a",
+ "2.6.0b-2",
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3",
+ "2.5.2b-1",
+ "2.7.10b+galaxy2",
+ "2.7.6a",
+ "2.7.10b+galaxy1"
+ ]
},
{
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"state": "missing"
}
],
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},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a",
"servers": [
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@@ -672307,6 +622493,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -672329,15 +622519,26 @@
},
{
"server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "2.7.8a+galaxy0",
+ "2.7.11a+galaxy0",
+ "2.7.2b"
+ ]
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "2.7.11a+galaxy1"
+ ]
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "2.7.8a"
+ ]
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -672359,15 +622560,11 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- },
{
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"state": "inexact",
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+ "2.7.11a+galaxy0"
]
},
{
@@ -672392,34 +622589,178 @@
},
{
"server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "2.7.8a+galaxy1"
+ ]
},
{
"server": "https://usegalaxy.be/",
"state": "exact",
- "version": "0.5.3.2"
+ "version": "2.7.7a"
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
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+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
+ "version": "2.7.7a"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "2.7.7a"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "2.7.7a"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "2.7.7a"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
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+ "version": "2.7.7a"
+ },
+ {
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+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
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+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
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+ {
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+ "state": "missing"
+ },
+ {
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+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
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+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
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+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
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},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.cz/",
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"versions": [
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- "1.1.5+galaxy0",
- "1.1.5+galaxy1"
+ "1.1.2+galaxy2"
]
},
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.5.3.2"
+ },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -672475,6 +622816,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -672527,10 +622872,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -672579,15 +622920,6 @@
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- "1.1.5+galaxy0",
- "1.1.5+galaxy1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -672633,6 +622965,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -672685,10 +623021,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -672737,23 +623069,14 @@
"state": "exact",
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- "server": "https://usegalaxy.fr/",
- "state": "inexact",
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- "1.1.5+galaxy1",
- "1.1.5+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.1.2+galaxy2",
- "1.1.2+galaxy1",
"0.5.5.1",
"1.1.2+galaxy0",
+ "1.1.2+galaxy1",
"0.5.5.2"
]
},
@@ -672763,8 +623086,8 @@
"versions": [
"1.1.2+galaxy2",
"0.5.5.1",
- "1.1.5+galaxy1",
"1.1.5+galaxy0",
+ "1.1.5+galaxy1",
"0.5.5.2"
]
},
@@ -672803,6 +623126,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -672855,10 +623182,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -672909,15 +623232,6 @@
"state": "exact",
"version": "0.5.5.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.1.2+galaxy2",
- "1.1.5+galaxy1",
- "1.1.5+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -672983,7 +623297,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 294,
- "visitors": 2247644,
+ "visitors": 2258371,
"workflows": [
{
"creators": [],
@@ -673089,7 +623403,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nList of FACS pairs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Flatten Collection\"];\n 0 -->|output| 3;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nCelSeq2: Single Batch mm10\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 4;\n 3 -->|output| 4;\n 2 -->|output| 4;\n 5[\"Column Join\"];\n 4 -->|9:out_counts| 5;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "CelSeq2: Multi Batch (mm10)",
"outputs": [
{
@@ -674150,7 +624464,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nBatch\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nBarcodes single-col\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"UMI-tools extract\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Alignment Choose a Genome\"];\n 2 -->|output| 4;\n 3 -->|out2| 4;\n 5[\"Filter\"];\n 4 -->|mapped_reads| 5;\n 6[\"featureCounts\"];\n 5 -->|out_file1| 6;\n 2 -->|output| 6;\n 7[\"UMI-tools count\"];\n 6 -->|output_bam| 7;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "CelSeq2: Single Batch (mm10)",
"outputs": [
{
@@ -675004,7 +625318,7 @@
"Interpret quality control (QC) plots to make informed decisions on cell thresholds",
"Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
],
- "pageviews": 4256,
+ "pageviews": 4277,
"priority": 1,
"pub_date": "2021-03-03",
"questions": [
@@ -675056,14 +625370,14 @@
"short_id": "T00245",
"short_tools": [
"sceasy_convert",
- "dropletutils_read_10x",
- "_ensembl_gtf2gene_list",
- "join1",
- "_salmon_kallisto_mtx_to_10x",
+ "alevin",
"Cut1",
"dropletutils_empty_drops",
+ "_salmon_kallisto_mtx_to_10x",
+ "join1",
+ "_ensembl_gtf2gene_list",
"_dropletBarcodePlot",
- "alevin"
+ "dropletutils_read_10x"
],
"slides": false,
"slides_recordings": false,
@@ -675105,6 +625419,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -675160,10 +625478,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -675210,11 +625524,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -675259,6 +625568,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -675311,10 +625624,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -675355,10 +625664,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -675401,6 +625706,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -675453,10 +625762,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -675497,10 +625802,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -675543,6 +625844,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -675595,10 +625900,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -675635,9 +625936,9 @@
"state": "inexact",
"versions": [
"0.14.1",
- "0.14.1.2+galaxy1",
"0.14.1.2",
- "1.3.0+galaxy2"
+ "1.3.0+galaxy2",
+ "0.14.1.2+galaxy1"
]
},
{
@@ -675650,10 +625951,6 @@
"state": "exact",
"version": "1.10.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -675699,6 +625996,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -675751,10 +626052,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -675796,10 +626093,6 @@
"state": "exact",
"version": "1.6.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -675844,6 +626137,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -675896,10 +626193,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -675942,10 +626235,6 @@
"state": "exact",
"version": "1.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -675990,6 +626279,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -676042,10 +626335,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -676088,10 +626377,6 @@
"state": "exact",
"version": "1.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -676136,6 +626421,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -676188,10 +626477,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -676234,10 +626519,6 @@
"state": "exact",
"version": "1.52.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -676285,6 +626566,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -676337,10 +626622,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -676382,10 +626663,6 @@
"state": "exact",
"version": "0.0.1+galaxy6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -676430,6 +626707,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -676482,10 +626763,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -676527,10 +626804,6 @@
"state": "exact",
"version": "0.0.7+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -676591,8 +626864,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 206,
- "visitors": 2722,
+ "visit_duration": 205,
+ "visitors": 2731,
"workflows": [
{
"creators": [
@@ -676743,7 +627016,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGTF file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"GTF2GeneList\"];\n 0 -->|output| 4;\n 5[\"Transcript-gene mapping\"];\n 1 -->|output| 5;\n 0 -->|output| 5;\n 773cb4ae-56c3-49c0-b582-ee69d620def3[\"Output\\nfasta_output\"];\n 5 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;\n style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;\n a30424b5-1ddc-4324-9ff6-dc5883adcce0[\"Output\\nfeature_annotation\"];\n 5 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;\n style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;\n 6[\"Alevin Processed\"];\n 2 -->|output| 6;\n 3 -->|output| 6;\n 5 -->|fasta_output| 6;\n 1 -->|output| 6;\n 5 -->|feature_annotation| 6;\n a87beb55-1baf-458e-bd09-bb5ac6ea6e9a[\"Output\\nraw_cb_frequency_txt\"];\n 6 --> a87beb55-1baf-458e-bd09-bb5ac6ea6e9a;\n style a87beb55-1baf-458e-bd09-bb5ac6ea6e9a stroke:#2c3143,stroke-width:4px;\n c9390a50-775c-4f0f-88e5-0984d570902c[\"Output\\nsalmon_quant_log\"];\n 6 --> c9390a50-775c-4f0f-88e5-0984d570902c;\n style c9390a50-775c-4f0f-88e5-0984d570902c stroke:#2c3143,stroke-width:4px;\n 2cebc438-ddc0-41e0-89ba-49b4bd3e2160[\"Output\\nquants_mat_mtx\"];\n 6 --> 2cebc438-ddc0-41e0-89ba-49b4bd3e2160;\n style 2cebc438-ddc0-41e0-89ba-49b4bd3e2160 stroke:#2c3143,stroke-width:4px;\n 89fa1aad-9ec6-4351-97d5-f05cac09e08e[\"Output\\nquants_mat_cols_txt\"];\n 6 --> 89fa1aad-9ec6-4351-97d5-f05cac09e08e;\n style 89fa1aad-9ec6-4351-97d5-f05cac09e08e stroke:#2c3143,stroke-width:4px;\n 3b3dda80-5d35-4c51-9ca0-90a2f909755f[\"Output\\nquants_mat_rows_txt\"];\n 6 --> 3b3dda80-5d35-4c51-9ca0-90a2f909755f;\n style 3b3dda80-5d35-4c51-9ca0-90a2f909755f stroke:#2c3143,stroke-width:4px;\n 7[\"Alevin - no processing\"];\n 2 -->|output| 7;\n 3 -->|output| 7;\n 5 -->|fasta_output| 7;\n 1 -->|output| 7;\n 5 -->|feature_annotation| 7;\n 25d4d8f6-d166-4470-80fe-d0fdb0702371[\"Output\\nquants_mat_rows_txt_1\"];\n 7 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;\n style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;\n d9ed1457-792b-4eaf-a9fc-2407bcd90da7[\"Output\\nquants_mat_mtx_1\"];\n 7 --> d9ed1457-792b-4eaf-a9fc-2407bcd90da7;\n style d9ed1457-792b-4eaf-a9fc-2407bcd90da7 stroke:#2c3143,stroke-width:4px;\n 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e[\"Output\\nquants_mat_cols_txt_1\"];\n 7 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;\n style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;\n 8[\"Droplet rank plot - raw barcodes\"];\n 6 -->|raw_cb_frequency_txt| 8;\n 9[\"Droplet rank plot - Alevin barcodes\"];\n 6 -->|quants_mat_mtx| 9;\n 10[\"salmonKallistoMtxTo10x\"];\n 7 -->|quants_mat_rows_txt| 10;\n 7 -->|quants_mat_cols_txt| 10;\n 7 -->|quants_mat_mtx| 10;\n 11[\"Join two Datasets\"];\n 10 -->|genes_out| 11;\n 4 -->|feature_annotation| 11;\n 12[\"Cut\"];\n 11 -->|out_file1| 12;\n 13[\"DropletUtils Read10x\"];\n 10 -->|barcodes_out| 13;\n 12 -->|out_file1| 13;\n 10 -->|matrix_out| 13;\n 14[\"DropletUtils emptyDrops\"];\n 13 -->|output_rds| 14;\n 15[\"SCEasy Converter\"];\n 14 -->|output_rdata| 15;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Generating a single cell matrix using Alevin",
"outputs": [
{
@@ -677127,24 +627400,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scater_create_qcmetric_ready_sce\n owner: iuc\n revisions: fd808de478b1\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_filter\n owner: iuc\n revisions: b7ea9f09c02f\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_dist_scatter\n owner: iuc\n revisions: 2e41b35b5bdd\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_pca\n owner: iuc\n revisions: 46fc6751d746\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json",
- "contributions": {
- "authorship": [
- "ethering",
- "nsoranzo"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "mtekman",
- "nsoranzo",
- "ethering",
- "bgruening",
- "lecorguille",
- "stephanierobin",
- "abretaud",
- "simonbray"
- ]
- },
"contributors": [
{
"id": "ethering",
@@ -677171,198 +627426,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
"twitter": "NicolaSoranzo",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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"scater_plot_pca",
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+ "scater_create_qcmetric_ready_sce",
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+ "scater_plot_dist_scatter"
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@@ -677495,6 +627558,10 @@
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],
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@@ -678800,7 +628842,7 @@
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"anndata_ops",
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@@ -678865,6 +628907,10 @@
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"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
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@@ -679161,6 +629194,10 @@
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- "state": "missing"
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- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
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"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
+ "state": "exact",
+ "version": "1.1.5"
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{
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@@ -680004,7 +629870,146 @@
"version": "1.1.5"
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{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.1.5"
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+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.1.5"
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+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.1.5"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
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+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
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+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
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+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
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+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.1.5"
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+ "state": "exact",
+ "version": "1.1.5"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "1.1.5"
},
@@ -680053,6 +630058,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680105,10 +630114,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
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{
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- "state": "missing"
- },
{
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"state": "missing"
@@ -680163,20 +630164,20 @@
"state": "inexact",
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+ "1.7.2+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0",
- "1.7.2+galaxy0"
+ "1.8.1+2+galaxy0"
]
},
{
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
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"1.8.1+galaxy0",
"1.8.1+galaxy93",
- "1.9.3+galaxy0",
- "1.8.1+1+galaxy1"
+ "1.8.1+1+galaxy1",
+ "1.8.1+galaxy91",
+ "1.9.3+galaxy0"
]
},
{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680261,10 +630266,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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"state": "missing"
@@ -680307,10 +630308,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
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"state": "missing"
@@ -680355,6 +630352,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680407,10 +630408,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -680452,10 +630449,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -680499,6 +630492,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680551,10 +630548,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -680599,10 +630592,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -680614,21 +630603,21 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.7.2+galaxy0",
+ "1.6.0+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0",
+ "1.7.2+galaxy0",
"1.8.1+galaxy9",
- "1.6.0+galaxy0"
+ "1.8.1+2+galaxy0"
]
},
{
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.8.1+1+galaxy0",
"1.8.1+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+galaxy9"
+ "1.8.1+galaxy9",
+ "1.8.1+1+galaxy0"
]
},
{
@@ -680661,6 +630650,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680713,10 +630706,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -680759,10 +630748,6 @@
"state": "exact",
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},
- {
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- "state": "missing"
- },
{
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"state": "missing"
@@ -680807,6 +630792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -680859,10 +630848,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -680907,13 +630892,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -680962,6 +630940,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681020,10 +631002,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -681075,11 +631053,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "1.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -681127,6 +631100,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681179,10 +631156,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -681216,10 +631189,10 @@
"state": "inexact",
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"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -681235,18 +631208,14 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"0.7.4+galaxy1",
"0.7.5+galaxy1",
- "0.6.22.post1+galaxy4",
- "0.7.5+galaxy0"
+ "0.7.5+galaxy0",
+ "0.6.22.post1+galaxy4"
]
},
{
@@ -681289,6 +631258,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681341,10 +631314,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -681378,10 +631347,10 @@
"state": "inexact",
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- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -681395,10 +631364,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -681444,6 +631409,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681500,10 +631469,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -681553,11 +631518,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -681603,6 +631563,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681662,10 +631626,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -681711,11 +631671,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -681765,6 +631720,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681822,10 +631781,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -681871,11 +631826,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -681925,6 +631875,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -681977,10 +631931,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -682013,13 +631963,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.2.1+1",
"1.2.1+3",
"1.2.1+2",
- "1.2.1+4",
+ "1.2.1+galaxy6",
"1.2.1+5",
"1.10.0+galaxy1",
- "1.2.1+galaxy6"
+ "1.2.1+1",
+ "1.2.1+4"
]
},
{
@@ -682032,11 +631982,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.10.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -682082,6 +632027,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -682134,10 +632083,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -682179,10 +632124,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -682254,8 +632195,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 98,
- "visitors": 1124,
+ "visit_duration": 97,
+ "visitors": 1149,
"workflows": [
{
"creators": [
@@ -682327,7 +632268,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Inspect AnnData\"];\n 0 -->|output| 1;\n 7bdb825c-6a89-4a34-bbd9-a79c309c9750[\"Output\\nInspect AnnData: obs\"];\n 1 --> 7bdb825c-6a89-4a34-bbd9-a79c309c9750;\n style 7bdb825c-6a89-4a34-bbd9-a79c309c9750 stroke:#2c3143,stroke-width:4px;\n 2[\"Inspect AnnData\"];\n 0 -->|output| 2;\n 79a2e3e5-4bd6-42de-864c-a5dc2412cb86[\"Output\\nInspect AnnData: var\"];\n 2 --> 79a2e3e5-4bd6-42de-864c-a5dc2412cb86;\n style 79a2e3e5-4bd6-42de-864c-a5dc2412cb86 stroke:#2c3143,stroke-width:4px;\n 3[\"Inspect AnnData\"];\n 0 -->|output| 3;\n 7a254954-7e32-4e8a-bd4c-a79abf9db8d8[\"Output\\nInspect AnnData: X\"];\n 3 --> 7a254954-7e32-4e8a-bd4c-a79abf9db8d8;\n style 7a254954-7e32-4e8a-bd4c-a79abf9db8d8 stroke:#2c3143,stroke-width:4px;\n 4[\"Transpose\"];\n 3 -->|X| 4;\n 5[\"Monocle3 create\"];\n 1 -->|obs| 5;\n 4 -->|out_file| 5;\n 2 -->|var| 5;\n 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c[\"Output\\nCDS Monocle file\"];\n 5 --> 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c;\n style 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "AnnData to Cell Data Set (CDS) conversion",
"outputs": [
{
@@ -682648,7 +632589,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Inspect AnnData\"];\n 0 -->|output| 1;\n 6d03d713-8d71-4f6a-9f83-cd999f423ebf[\"Output\\nInspect AnnData: obs\"];\n 1 --> 6d03d713-8d71-4f6a-9f83-cd999f423ebf;\n style 6d03d713-8d71-4f6a-9f83-cd999f423ebf stroke:#2c3143,stroke-width:4px;\n 2[\"Inspect AnnData\"];\n 0 -->|output| 2;\n ea025a8a-6f3a-4e38-a3af-db406886c7de[\"Output\\nInspect AnnData: X\"];\n 2 --> ea025a8a-6f3a-4e38-a3af-db406886c7de;\n style ea025a8a-6f3a-4e38-a3af-db406886c7de stroke:#2c3143,stroke-width:4px;\n 3[\"Transpose\"];\n 2 -->|X| 3;\n 4[\"DropletUtils\"];\n 3 -->|out_file| 4;\n 5[\"Seurat Read10x\"];\n 4 -->|barcodes_out| 5;\n 4 -->|genes_out| 5;\n 4 -->|matrix_out| 5;\n 1 -->|obs| 5;\n e5fec5dc-4706-48e5-8326-05e70290552d[\"Output\\nConverted Seurat object\"];\n 5 --> e5fec5dc-4706-48e5-8326-05e70290552d;\n style e5fec5dc-4706-48e5-8326-05e70290552d stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "AnnData to Seurat conversion",
"outputs": [
{
@@ -682954,7 +632895,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Parameter\\nCell ID column\"];\n style 1 fill:#ded,stroke:#393,stroke-width:4px;\n 2[\"Inspect AnnData\"];\n 0 -->|output| 2;\n 8b9200c2-96e6-40fa-a8e9-1e99638c733f[\"Output\\nInspect AnnData: obs\"];\n 2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f;\n style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px;\n 3[\"Inspect AnnData\"];\n 0 -->|output| 3;\n 9fc4ce5a-8384-484d-b1cd-c0f5137cf821[\"Output\\nInspect AnnData: X\"];\n 3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821;\n style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px;\n 4[\"Transpose\"];\n 3 -->|X| 4;\n 5[\"DropletUtils\"];\n 4 -->|out_file| 5;\n 6[\"DropletUtils Read10x\"];\n 1 -->|output| 6;\n 2 -->|obs| 6;\n 5 -->|barcodes_out| 6;\n 5 -->|genes_out| 6;\n 5 -->|matrix_out| 6;\n 3256e23f-2026-407d-aa25-0f8c0f3ae3f7[\"Output\\nConverted SCE object\"];\n 6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7;\n style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "AnnData to SingleCellExperiment (SCE) conversion",
"outputs": [
{
@@ -683230,19 +633171,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_construct_eset\n owner: bgruening\n revisions: 2cfd0db49bbc\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_construct_eset\n owner: bgruening\n revisions: 7ffaa0968da3\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_deconvolution\n owner: bgruening\n revisions: 56371b5a2da9\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_inspect_eset\n owner: bgruening\n revisions: 8c64a2da3869\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json",
- "contributions": {
- "authorship": [
- "mtekman",
- "nomadscientist"
- ],
- "reviewing": [
- "hexylena",
- "mtekman",
- "shiltemann",
- "nomadscientist",
- "bgruening"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -683276,132 +633204,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
"twitter": "WendiBacon1",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- ],
- "bio": "Senior Lecturer at The Open University",
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- "twitter": "WendiBacon1",
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- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/single-cell/tutorials/bulk-music",
@@ -683444,7 +633246,7 @@
"Inspect these objects for various properties",
"Measure the abundance of certain cell type cluster markers compared to others"
],
- "pageviews": 3814,
+ "pageviews": 3821,
"priority": 1,
"pub_date": "2022-02-11",
"questions": [
@@ -683536,6 +633338,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -683591,10 +633397,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -683641,11 +633443,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -683690,6 +633487,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -683742,10 +633543,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -683788,10 +633585,6 @@
"state": "exact",
"version": "0.1.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -683836,6 +633629,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -683888,10 +633685,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -683934,10 +633727,6 @@
"state": "exact",
"version": "0.1.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -683982,6 +633771,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -684034,10 +633827,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -684080,10 +633869,6 @@
"state": "exact",
"version": "0.1.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -684128,6 +633913,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -684180,10 +633969,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -684226,10 +634011,6 @@
"state": "exact",
"version": "0.1.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -684285,7 +634066,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 98,
- "visitors": 2982,
+ "visitors": 2988,
"workflows": [
{
"creators": [],
@@ -684621,7 +634402,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nscRNA Assay Tabular\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nscRNA Phenotype Tabular\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nscRNA Metadata\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nBulk RNA Assay Tabular\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nBulk RNA Annotation\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Parameter\\nCell Types List\"];\n style 5 fill:#ded,stroke:#393,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nCell Markers C1\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nCell Markers C2\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"Construct scRNA ESet Object\"];\n 0 -->|output| 8;\n 2 -->|output| 8;\n 1 -->|output| 8;\n 872b3dd2-322c-47cc-b5b9-071a9f939320[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n 8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320;\n style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px;\n 9[\"Construct Bulk RNA ESet Object\"];\n 4 -->|output| 9;\n 3 -->|output| 9;\n 10[\"Extract Cell Types\"];\n 8 -->|out_rds| 10;\n 11[\"Extract General Info\"];\n 8 -->|out_rds| 11;\n 1733593f-847d-4adb-91f4-fd78c077b074[\"Output\\nInspect Expression Set Object on input dataset(s): Inspection Result\"];\n 11 --> 1733593f-847d-4adb-91f4-fd78c077b074;\n style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px;\n 12[\"Extract General Info Bulk\"];\n 9 -->|out_rds| 12;\n 13[\"Music: Estimate Cell Proportions\"];\n 9 -->|out_rds| 13;\n 5 -->|output| 13;\n 8 -->|out_rds| 13;\n 14[\"Music: Compute Dendrogram\"];\n 9 -->|out_rds| 14;\n 6 -->|output| 14;\n 7 -->|output| 14;\n 8 -->|out_rds| 14;\n df2e83a5-ac67-460f-8b0f-ac3f3b63280f[\"Output\\nMuSiC on input dataset(s): PDF Plots\"];\n 14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f;\n style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "MuSiC Workflow",
"outputs": [
{
@@ -685467,27 +635248,6 @@
}
],
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
- "contributions": {
- "authorship": [
- "mtekman",
- "hrhotz",
- "blankenberg",
- "nomadscientist",
- "pavanvidem"
- ],
- "reviewing": [
- "bgruening",
- "dirowa",
- "shiltemann",
- "hexylena",
- "pavanvidem",
- "nomadscientist",
- "mtekman",
- "bebatut",
- "hrhotz",
- "gallardoalba"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -685566,228 +635326,15 @@
"orcid": "0000-0002-5192-126X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
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- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "email": "D.vrins@live.nl",
- "former_affiliations": [
- "avans-atgm"
- ],
- "id": "dirowa",
- "joined": "2021-10",
- "linkedin": "Donny Vrins",
- "name": "Donny Vrins",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
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],
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],
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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- "1.9.3+galaxy0",
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+ "1.8.1+1+galaxy1",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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@@ -690116,6 +639422,10 @@
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{
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{
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@@ -690264,6 +639565,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -690364,10 +639665,6 @@
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- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -690384,8 +639681,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.8.1+1+galaxy0"
+ "1.8.1+1+galaxy0",
+ "1.9.3+galaxy0"
]
},
{
@@ -690418,6 +639715,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -690470,10 +639771,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -690518,13 +639815,6 @@
"state": "exact",
"version": "3.2.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.0.4+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -690573,6 +639863,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -690625,10 +639919,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -690671,11 +639961,6 @@
"state": "exact",
"version": "4.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -690720,6 +640005,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -690776,10 +640065,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -690827,11 +640112,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -690877,6 +640157,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -690929,10 +640213,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -690974,10 +640254,6 @@
"state": "exact",
"version": "0.0.7+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -691040,8 +640316,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 288,
- "visitors": 335,
+ "visit_duration": 282,
+ "visitors": 342,
"workflows": [
{
"creators": [
@@ -691112,7 +640388,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"EBI SCXA Data Retrieval\"];\n 0 -->|output| 1;\n 2[\"Rename batch numbers\"];\n 1 -->|design_tsv| 2;\n 3[\"Mito genes check\"];\n 1 -->|genes_tsv| 3;\n b0762cfd-58bd-4c39-ae41-2dca4289c541[\"Output\\nMito genes check\"];\n 3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;\n style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;\n 4[\"Rename cell metadata headers\"];\n 2 -->|out_file1| 4;\n 5[\"Create AnnData\"];\n 1 -->|barcode_tsv| 5;\n 4 -->|outfile| 5;\n 1 -->|genes_tsv| 5;\n 1 -->|matrix_mtx| 5;\n 938cd594-61cf-4037-a58b-c09c065db505[\"Output\\nAnnData object\"];\n 5 --> 938cd594-61cf-4037-a58b-c09c065db505;\n style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;\n 6[\"Seurat Read10x\"];\n 1 -->|barcode_tsv| 6;\n 1 -->|genes_tsv| 6;\n 1 -->|matrix_mtx| 6;\n 4 -->|outfile| 6;\n c24e9d83-c175-40a2-9c36-eeb486fe323e[\"Output\\nSeurat object\"];\n 6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;\n style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;\n 7[\"AnnData Operations\"];\n 5 -->|output_h5ad| 7;\n b47f801f-bedb-4136-a5e9-378a815a1799[\"Output\\nMito-counted AnnData for downstream analysis\"];\n 7 --> b47f801f-bedb-4136-a5e9-378a815a1799;\n style b47f801f-bedb-4136-a5e9-378a815a1799 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
"outputs": [
{
@@ -691718,7 +640994,7 @@
"Appraise data outputs and decisions",
"Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
],
- "pageviews": 2759,
+ "pageviews": 2773,
"priority": 2,
"pub_date": "2023-10-02",
"questions": [
@@ -691808,7 +641084,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 58,
- "visitors": 2415,
+ "visitors": 2429,
"zenodo_link": "https://zenodo.org/record/7053673"
},
{
@@ -692206,7 +641482,7 @@
"Combine data matrices from different samples in the same experiment",
"Label the metadata for downstream processing"
],
- "pageviews": 2789,
+ "pageviews": 2805,
"priority": 2,
"pub_date": "2022-09-08",
"questions": [
@@ -692255,14 +641531,14 @@
],
"short_id": "T00246",
"short_tools": [
- "scanpy_read_10x",
- "anndata_inspect",
- "anndata_manipulate",
- "retrieve_scxa",
+ "Cut1",
"tp_replace_in_column",
"anndata_ops",
- "Cut1",
- "Paste1"
+ "retrieve_scxa",
+ "anndata_inspect",
+ "Paste1",
+ "scanpy_read_10x",
+ "anndata_manipulate"
],
"slides": false,
"slides_recordings": false,
@@ -692310,6 +641586,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -692365,10 +641645,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -692415,11 +641691,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -692464,6 +641735,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -692516,10 +641791,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -692560,10 +641831,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -692606,6 +641873,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -692658,10 +641929,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -692702,10 +641969,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -692748,6 +642011,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -692806,10 +642073,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -692865,11 +642128,6 @@
"state": "exact",
"version": "9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -692925,6 +642183,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -692977,10 +642239,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -693022,10 +642280,6 @@
"state": "exact",
"version": "1.9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -693070,6 +642324,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -693122,10 +642380,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -693168,11 +642422,6 @@
"state": "exact",
"version": "v0.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "v0.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -693218,6 +642467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -693270,10 +642523,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -693318,10 +642567,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -693338,8 +642583,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.8.1+1+galaxy0"
+ "1.8.1+1+galaxy0",
+ "1.9.3+galaxy0"
]
},
{
@@ -693372,6 +642617,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -693424,10 +642673,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -693461,10 +642706,10 @@
"state": "inexact",
"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -693480,18 +642725,14 @@
"state": "exact",
"version": "0.10.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"0.7.4+galaxy1",
"0.7.5+galaxy1",
- "0.6.22.post1+galaxy4",
- "0.7.5+galaxy0"
+ "0.7.5+galaxy0",
+ "0.6.22.post1+galaxy4"
]
},
{
@@ -693534,6 +642775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -693586,10 +642831,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -693622,10 +642863,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -693641,17 +642882,13 @@
"state": "exact",
"version": "0.10.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"0.7.5+galaxy1",
- "0.7.5+galaxy0",
"0.6.22.post1+galaxy4",
+ "0.7.5+galaxy0",
"0.7.4+galaxy1"
]
},
@@ -693712,7 +642949,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 145,
- "visitors": 1941,
+ "visitors": 1952,
"workflows": [
{
"creators": [
@@ -693937,7 +643174,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nN701\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nN702\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nN703\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nN704\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nN705\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nN706\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nN707\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"Concatenating Datasets\"];\n 0 -->|output| 7;\n 1 -->|output| 7;\n 2 -->|output| 7;\n 3 -->|output| 7;\n 4 -->|output| 7;\n 5 -->|output| 7;\n 6 -->|output| 7;\n 168d4710-570a-43b1-998a-2164154eebc5[\"Output\\nCombined Object\"];\n 7 --> 168d4710-570a-43b1-998a-2164154eebc5;\n style 168d4710-570a-43b1-998a-2164154eebc5 stroke:#2c3143,stroke-width:4px;\n 8[\"Inspect AnnData\"];\n 7 -->|anndata| 8;\n 9[\"Inspect AnnData\"];\n 7 -->|anndata| 9;\n 10[\"Inspect AnnData\"];\n 7 -->|anndata| 10;\n 11[\"Replace Text\"];\n 9 -->|obs| 11;\n 12[\"Replace Text\"];\n 9 -->|obs| 12;\n 13[\"Cut\"];\n 11 -->|outfile| 13;\n 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea[\"Output\\nSex metadata\"];\n 13 --> 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea;\n style 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea stroke:#2c3143,stroke-width:4px;\n 14[\"Cut\"];\n 12 -->|outfile| 14;\n 6f55548b-5ded-42b8-b2f7-c7f1a327a068[\"Output\\nGenotype metadata\"];\n 14 --> 6f55548b-5ded-42b8-b2f7-c7f1a327a068;\n style 6f55548b-5ded-42b8-b2f7-c7f1a327a068 stroke:#2c3143,stroke-width:4px;\n 15[\"Paste\"];\n 14 -->|out_file1| 15;\n 13 -->|out_file1| 15;\n 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6[\"Output\\nCell metadata\"];\n 15 --> 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6;\n style 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6 stroke:#2c3143,stroke-width:4px;\n 16[\"Adding in cell metadata\"];\n 7 -->|anndata| 16;\n 15 -->|out_file1| 16;\n 2720386c-7273-49d6-abb0-9bd14f6cb68c[\"Output\\nAnnData with Cell Metadata\"];\n 16 --> 2720386c-7273-49d6-abb0-9bd14f6cb68c;\n style 2720386c-7273-49d6-abb0-9bd14f6cb68c stroke:#2c3143,stroke-width:4px;\n 17[\"Batching Cell Metadata\"];\n 16 -->|anndata| 17;\n b950c8db-abe1-4cb0-af58-d291d3b74a83[\"Output\\nBatched Object\"];\n 17 --> b950c8db-abe1-4cb0-af58-d291d3b74a83;\n style b950c8db-abe1-4cb0-af58-d291d3b74a83 stroke:#2c3143,stroke-width:4px;\n 18[\"Calculating mitochondrial \"];\n 17 -->|anndata| 18;\n 2417284d-8252-43ff-84bf-6f15ef11cd05[\"Output\\nAnnotated AnnData\"];\n 18 --> 2417284d-8252-43ff-84bf-6f15ef11cd05;\n style 2417284d-8252-43ff-84bf-6f15ef11cd05 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Combining datasets after pre-processing",
"outputs": [
{
@@ -694645,7 +643882,7 @@
"Use the cell cycle genes to regress out the effects of the cell cycle",
"Create PCA plots to understand the impact of the regression"
],
- "pageviews": 1889,
+ "pageviews": 1904,
"priority": 2,
"pub_date": "2023-01-25",
"questions": [
@@ -694664,17 +643901,17 @@
],
"short_id": "T00248",
"short_tools": [
+ "cat1",
+ "scanpy_regress_variable",
+ "sort1",
"tp_easyjoin_tool",
"table_compute",
- "addValue",
"anndata_inspect",
- "anndata_manipulate",
- "scanpy_cluster_reduce_dimension",
"scanpy_plot",
- "sort1",
- "cat1",
+ "anndata_manipulate",
"scanpy_inspect",
- "scanpy_regress_variable"
+ "addValue",
+ "scanpy_cluster_reduce_dimension"
],
"slides": false,
"slides_recordings": false,
@@ -694716,6 +643953,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -694771,10 +644012,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -694821,11 +644058,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -694870,6 +644102,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -694922,10 +644158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -694966,10 +644198,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -695012,6 +644240,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -695064,10 +644296,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -695108,10 +644336,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -695154,6 +644378,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695208,10 +644436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -695258,11 +644482,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -695308,6 +644527,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695361,10 +644584,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -695411,11 +644630,6 @@
"state": "exact",
"version": "1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -695460,6 +644674,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695512,10 +644730,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -695557,10 +644771,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -695569,8 +644779,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.8.1+galaxy9"
+ "1.8.1+galaxy9",
+ "1.9.3+galaxy0"
]
},
{
@@ -695608,6 +644818,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695660,10 +644874,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -695697,10 +644907,10 @@
"state": "inexact",
"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -695714,10 +644924,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -695763,6 +644969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695815,10 +645025,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -695851,10 +645057,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -695868,10 +645074,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -695917,6 +645119,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -695969,10 +645175,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -696005,11 +645207,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2",
- "1.4.4+galaxy0"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy1"
]
},
{
@@ -696022,10 +645224,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -696071,6 +645269,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -696123,10 +645325,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -696161,9 +645359,9 @@
"versions": [
"1.4.4+galaxy0",
"1.4.4.post1+galaxy0",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy2",
- "1.4+galaxy0"
+ "1.4.4.post1+galaxy2"
]
},
{
@@ -696176,10 +645374,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -696225,6 +645419,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -696277,10 +645475,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -696313,10 +645507,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -696330,10 +645524,6 @@
"state": "exact",
"version": "1.7.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -696379,6 +645569,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -696433,10 +645627,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -696483,11 +645673,6 @@
"state": "exact",
"version": "1.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -696551,7 +645736,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 47,
- "visitors": 1580,
+ "visitors": 1594,
"workflows": [
{
"creators": [],
@@ -696680,7 +645865,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData After QC, normalisation, scaling\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nS Phase Genes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nG2M Phase Genes\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nPasted Entry\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Inspect AnnData\"];\n 0 -->|output| 4;\n 5[\"All Cell Cycle Genes Concatenate S and G2M Genes\"];\n 1 -->|output| 5;\n 2 -->|output| 5;\n 6[\"Inspect and manipulate\"];\n 0 -->|output| 6;\n 2 -->|output| 6;\n 1 -->|output| 6;\n 7[\"Table Compute\"];\n 4 -->|var| 7;\n 8[\"Add column\"];\n 5 -->|out_file1| 8;\n 9[\"Scanpy RegressOut\"];\n 6 -->|anndata_out| 9;\n 026b02d3-97ee-4847-9347-40773ab76356[\"Output\\nScanpy RegressOut on input dataset(s): Regressed out AnnData\"];\n 9 --> 026b02d3-97ee-4847-9347-40773ab76356;\n style 026b02d3-97ee-4847-9347-40773ab76356 stroke:#2c3143,stroke-width:4px;\n 10[\"Add column\"];\n 7 -->|table| 10;\n 11[\"Join\"];\n 10 -->|out_file1| 11;\n 8 -->|out_file1| 11;\n 12[\"Sort\"];\n 11 -->|output| 12;\n 13[\"Table Compute\"];\n 12 -->|out_file1| 13;\n 14[\"Concatenate datasets\"];\n 3 -->|output| 14;\n 13 -->|table| 14;\n 15[\"Manipulate AnnData\"];\n 6 -->|anndata_out| 15;\n 14 -->|out_file1| 15;\n 16[\"Manipulate AnnData\"];\n 9 -->|output_h5ad| 16;\n 14 -->|out_file1| 16;\n 17[\"Manipulate AnnData\"];\n 15 -->|anndata| 17;\n 18[\"Manipulate AnnData\"];\n 16 -->|anndata| 18;\n 19[\"Cluster, infer trajectories and embed\"];\n 17 -->|anndata| 19;\n 20[\"Cluster, infer trajectories and embed\"];\n 18 -->|anndata| 20;\n 09d97ef7-ed92-4d90-a597-2032581c2d4a[\"Output\\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix\"];\n 20 --> 09d97ef7-ed92-4d90-a597-2032581c2d4a;\n style 09d97ef7-ed92-4d90-a597-2032581c2d4a stroke:#2c3143,stroke-width:4px;\n 21[\"Plot\"];\n 19 -->|anndata_out| 21;\n 22[\"Plot\"];\n 20 -->|anndata_out| 22;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Cell Cycle Regression Workflow",
"outputs": [
{
@@ -697592,22 +646777,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n owner: iuc\n revisions: 562f3c677828\n tool_panel_section_label: Join, Subtract and Group\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n owner: iuc\n revisions: 22c2a1ac7ae3\n tool_panel_section_label: Join, Subtract and Group\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_clustering\n owner: iuc\n revisions: a4b734cd253b\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_filtnormconf\n owner: iuc\n revisions: 43c146e25a43\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspectclusters\n owner: iuc\n revisions: 41f34e925bd5\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspecttrajectory\n owner: iuc\n revisions: c8434a623268\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_trajectory\n owner: iuc\n revisions: 72979cac22b2\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json",
- "contributions": {
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- "mtekman",
- "astrovsky01"
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- "reviewing": [
- "shiltemann",
- "hexylena",
- "bgruening",
- "bebatut",
- "mtekman",
- "stephanierobin",
- "abretaud",
- "simonbray"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -697632,193 +646801,12 @@
"orcid": "0000-0002-7901-7109",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
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],
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"edam_operation": [
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"Molecular dynamics",
+ "Expression profile clustering",
"Expression analysis"
],
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],
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"priority": 2,
"pub_date": "2019-03-25",
"questions": [
@@ -697885,15 +646873,15 @@
],
"short_id": "T00253",
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"raceid_clustering",
"datamash_ops",
+ "datamash_transpose",
"raceid_inspecttrajectory",
- "raceid_inspectclusters",
"raceid_filtnormconf",
- "tp_sed_tool",
+ "tp_head_tool",
"raceid_trajectory",
- "datamash_transpose",
- "tp_head_tool"
+ "raceid_inspectclusters"
],
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"slides_recordings": false,
@@ -697924,6 +646912,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
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{
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"url": "https://usegalaxy.no/",
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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"state": "missing"
@@ -698504,6 +647475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -698646,6 +647613,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
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@@ -698788,6 +647751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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@@ -698842,10 +647809,6 @@
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@@ -698942,6 +647900,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
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@@ -698996,10 +647958,6 @@
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"state": "exact",
@@ -699096,6 +648049,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
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"state": "exact",
@@ -699253,6 +648201,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
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@@ -699312,10 +648264,6 @@
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{
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"state": "exact",
@@ -699409,6 +648352,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
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@@ -699461,10 +648408,6 @@
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{
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@@ -699497,8 +648440,8 @@
"server": "https://usegalaxy.be/",
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+ "3.0.2.1",
+ "3.1"
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@@ -699562,6 +648501,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
+ },
{
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@@ -699650,10 +648589,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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+ "3.0.2.2",
"3.1",
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- "3.0.2.2"
+ "3.0.2.3",
+ "3.0.2.1"
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{
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@@ -699720,6 +648652,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
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@@ -699772,10 +648708,6 @@
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"server": "https://usegalaxy.be/",
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"versions": [
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+ "3.1",
+ "3.0.2.1"
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},
{
@@ -699824,10 +648756,6 @@
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},
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{
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@@ -699877,6 +648805,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -699929,10 +648861,6 @@
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@@ -699981,10 +648909,6 @@
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{
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"state": "exact",
@@ -700034,6 +648958,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
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@@ -700086,10 +649014,6 @@
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"server": "https://usegalaxy.be/",
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"versions": [
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+ "3.1",
+ "3.0.2.1"
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},
{
@@ -700138,10 +649062,6 @@
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{
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@@ -700205,8 +649125,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 81,
- "visitors": 865,
+ "visit_duration": 80,
+ "visitors": 871,
"workflows": [
{
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@@ -700269,7 +649189,7 @@
],
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- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "RaceID Workflow",
"outputs": [
{
@@ -701112,12 +650032,12 @@
"dir": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2",
"edam_operation": [
"Essential dynamics",
- "Dimensionality reduction",
- "Sequence alignment",
- "Differential gene expression analysis",
"Gene expression profiling",
- "Read mapping",
"Generation",
+ "Read mapping",
+ "Differential gene expression analysis",
+ "Sequence alignment",
+ "Dimensionality reduction",
"Genome indexing"
],
"edam_topic": [],
@@ -701148,7 +650068,7 @@
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],
- "pageviews": 655,
+ "pageviews": 679,
"priority": 2,
"pub_date": "2024-07-11",
"questions": [
@@ -701172,21 +650092,21 @@
],
"short_id": "T00445",
"short_tools": [
- "bwa_mem",
- "snapatac2_clustering",
"scanpy_normalize",
- "anndata_inspect",
+ "scanpy_filter",
+ "Cut1",
"snapatac2_preprocessing",
- "anndata_manipulate",
"snapatac2_plotting",
- "scanpy_plot",
- "scanpy_inspect",
- "scanpy_filter",
"fasta_compute_length",
"snapatac2_peaks_and_motif",
- "anndata_ops",
+ "bwa_mem",
"replace_column_with_key_value_file",
- "Cut1"
+ "anndata_ops",
+ "anndata_inspect",
+ "snapatac2_clustering",
+ "scanpy_plot",
+ "anndata_manipulate",
+ "scanpy_inspect"
],
"slides": false,
"slides_recordings": false,
@@ -701217,6 +650137,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -701272,10 +650196,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -701322,11 +650242,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -701371,6 +650286,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -701423,10 +650342,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -701467,10 +650382,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -701513,6 +650424,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -701566,10 +650481,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -701614,11 +650525,6 @@
"state": "exact",
"version": "0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -701664,6 +650570,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -701725,10 +650635,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -701779,11 +650685,6 @@
"state": "exact",
"version": "0.7.18"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.18"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -701835,6 +650736,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -701888,10 +650793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -701933,10 +650834,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -701980,154 +650877,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.0.3"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "1.0.3"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -702160,7 +650910,8 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "exact",
+ "version": "1.0.3"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -702183,7 +650934,148 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.0.3"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.0.3"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -702227,10 +651119,6 @@
"state": "exact",
"version": "1.9.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -702275,6 +651163,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -702327,10 +651219,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -702364,10 +651252,10 @@
"state": "inexact",
"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -702383,18 +651271,14 @@
"state": "exact",
"version": "0.10.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"0.7.4+galaxy1",
"0.7.5+galaxy1",
- "0.6.22.post1+galaxy4",
- "0.7.5+galaxy0"
+ "0.7.5+galaxy0",
+ "0.6.22.post1+galaxy4"
]
},
{
@@ -702437,6 +651321,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -702489,10 +651377,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -702525,10 +651409,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -702544,17 +651428,13 @@
"state": "exact",
"version": "0.10.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"0.7.5+galaxy1",
- "0.7.5+galaxy0",
"0.6.22.post1+galaxy4",
+ "0.7.5+galaxy0",
"0.7.4+galaxy1"
]
},
@@ -702598,6 +651478,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -702650,10 +651534,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -702686,11 +651566,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4+galaxy0",
- "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy1",
"1.4+galaxy0",
- "1.4.4.post1+galaxy2"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
+ "1.4.4.post1+galaxy0"
]
},
{
@@ -702705,10 +651585,6 @@
"state": "exact",
"version": "1.9.6+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -702757,6 +651633,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -702809,10 +651689,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -702847,9 +651723,9 @@
"versions": [
"1.4.4+galaxy0",
"1.4.4.post1+galaxy0",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy2",
- "1.4+galaxy0"
+ "1.4.4.post1+galaxy2"
]
},
{
@@ -702864,10 +651740,6 @@
"state": "exact",
"version": "1.9.6+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -702916,6 +651788,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -702968,10 +651844,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703004,11 +651876,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy2",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy0",
- "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
"1.4.4.post1+galaxy1",
- "1.4+galaxy0"
+ "1.4.4+galaxy0"
]
},
{
@@ -703023,10 +651895,6 @@
"state": "exact",
"version": "1.9.6+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -703075,6 +651943,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -703127,10 +651999,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703163,10 +652031,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -703182,10 +652050,6 @@
"state": "exact",
"version": "1.9.6+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -703234,6 +652098,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -703286,10 +652154,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703331,10 +652195,6 @@
"state": "exact",
"version": "2.6.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -703379,6 +652239,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -703431,10 +652295,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703476,10 +652336,6 @@
"state": "exact",
"version": "2.6.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -703524,6 +652380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -703576,10 +652436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703621,10 +652477,6 @@
"state": "exact",
"version": "2.6.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -703669,6 +652521,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -703721,10 +652577,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -703766,10 +652618,6 @@
"state": "exact",
"version": "2.6.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -703838,8 +652686,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 68,
- "visitors": 514,
+ "visit_duration": 70,
+ "visitors": 537,
"workflows": [
{
"creators": [
@@ -704047,7 +652895,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nFragment_file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ngene_annotation\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nBam-file\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nReplace_file\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"pp.import_data\"];\n 1 -->|output| 6;\n 0 -->|output| 6;\n 7[\"pp.make_fragment_file\"];\n 3 -->|output| 7;\n 8[\"pl.frag_size_distr\"];\n 6 -->|anndata_out| 8;\n 265d6020-44e2-408c-9eb6-02cbc9ac23a7[\"Output\\nplot frag_size\"];\n 8 --> 265d6020-44e2-408c-9eb6-02cbc9ac23a7;\n style 265d6020-44e2-408c-9eb6-02cbc9ac23a7 stroke:#2c3143,stroke-width:4px;\n 9[\"pl.frag_size_distr_log\"];\n 6 -->|anndata_out| 9;\n a37cd3c3-e07e-4bea-899f-ee44cee8370b[\"Output\\nplot log frag_size\"];\n 9 --> a37cd3c3-e07e-4bea-899f-ee44cee8370b;\n style a37cd3c3-e07e-4bea-899f-ee44cee8370b stroke:#2c3143,stroke-width:4px;\n 10[\"metrics.tsse\"];\n 6 -->|anndata_out| 10;\n 2 -->|output| 10;\n 233284e5-c184-4330-a1d3-2d03951c4ce7[\"Output\\nanndata tsse\"];\n 10 --> 233284e5-c184-4330-a1d3-2d03951c4ce7;\n style 233284e5-c184-4330-a1d3-2d03951c4ce7 stroke:#2c3143,stroke-width:4px;\n 11[\"pp.import_data-sorted_by_barcodes\"];\n 1 -->|output| 11;\n 7 -->|fragments_out| 11;\n 50ef9fe7-bb08-4957-bc45-079ed78f9ee8[\"Output\\nanndata\"];\n 11 --> 50ef9fe7-bb08-4957-bc45-079ed78f9ee8;\n style 50ef9fe7-bb08-4957-bc45-079ed78f9ee8 stroke:#2c3143,stroke-width:4px;\n 12[\"pl.tsse\"];\n 10 -->|anndata_out| 12;\n 9a5c0f9c-0423-4822-871e-ba8317f2fa7b[\"Output\\nplot tsse\"];\n 12 --> 9a5c0f9c-0423-4822-871e-ba8317f2fa7b;\n style 9a5c0f9c-0423-4822-871e-ba8317f2fa7b stroke:#2c3143,stroke-width:4px;\n 13[\"pp.filter_cells\"];\n 10 -->|anndata_out| 13;\n b58dc4ad-6bf0-4f31-99f4-4f8deb13427c[\"Output\\nanndata filter cells\"];\n 13 --> b58dc4ad-6bf0-4f31-99f4-4f8deb13427c;\n style b58dc4ad-6bf0-4f31-99f4-4f8deb13427c stroke:#2c3143,stroke-width:4px;\n 14[\"pp.add_tile_matrix\"];\n 13 -->|anndata_out| 14;\n d4b64fc4-fd35-4781-b799-0d07fe8fe438[\"Output\\nanndata tile matrix\"];\n 14 --> d4b64fc4-fd35-4781-b799-0d07fe8fe438;\n style d4b64fc4-fd35-4781-b799-0d07fe8fe438 stroke:#2c3143,stroke-width:4px;\n 15[\"pp.select_features\"];\n 14 -->|anndata_out| 15;\n f531f6bd-3fc6-48b9-bb33-66de7928e670[\"Output\\nanndata select features\"];\n 15 --> f531f6bd-3fc6-48b9-bb33-66de7928e670;\n style f531f6bd-3fc6-48b9-bb33-66de7928e670 stroke:#2c3143,stroke-width:4px;\n 16[\"pp.scrublet\"];\n 15 -->|anndata_out| 16;\n 5b17aa3a-3694-440f-9022-cf9761feb760[\"Output\\nanndata scrublet\"];\n 16 --> 5b17aa3a-3694-440f-9022-cf9761feb760;\n style 5b17aa3a-3694-440f-9022-cf9761feb760 stroke:#2c3143,stroke-width:4px;\n 17[\"pp.filter_doublets\"];\n 16 -->|anndata_out| 17;\n 3838cf9d-a018-4aa7-8852-893b2f60ec2a[\"Output\\nanndata filter doublets\"];\n 17 --> 3838cf9d-a018-4aa7-8852-893b2f60ec2a;\n style 3838cf9d-a018-4aa7-8852-893b2f60ec2a stroke:#2c3143,stroke-width:4px;\n 18[\"tl.spectral\"];\n 17 -->|anndata_out| 18;\n 77883516-8ac4-40b5-8b75-5750639d9fc4[\"Output\\nanndata spectral\"];\n 18 --> 77883516-8ac4-40b5-8b75-5750639d9fc4;\n style 77883516-8ac4-40b5-8b75-5750639d9fc4 stroke:#2c3143,stroke-width:4px;\n 19[\"tl.umap\"];\n 18 -->|anndata_out| 19;\n 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad[\"Output\\nanndata umap\"];\n 19 --> 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad;\n style 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad stroke:#2c3143,stroke-width:4px;\n 20[\"pp.knn\"];\n 19 -->|anndata_out| 20;\n b7ebe580-9938-48e5-8718-4df197126615[\"Output\\nanndata knn\"];\n 20 --> b7ebe580-9938-48e5-8718-4df197126615;\n style b7ebe580-9938-48e5-8718-4df197126615 stroke:#2c3143,stroke-width:4px;\n 21[\"tl.leiden\"];\n 20 -->|anndata_out| 21;\n 9970eb96-013b-4d97-bbbf-2d1f4663b73c[\"Output\\nanndata_leiden_clustering\"];\n 21 --> 9970eb96-013b-4d97-bbbf-2d1f4663b73c;\n style 9970eb96-013b-4d97-bbbf-2d1f4663b73c stroke:#2c3143,stroke-width:4px;\n 22[\"pl.umap\"];\n 21 -->|anndata_out| 22;\n 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9[\"Output\\numap_leiden-clusters\"];\n 22 --> 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9;\n style 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9 stroke:#2c3143,stroke-width:4px;\n 23[\"make_gene_matrix\"];\n 21 -->|anndata_out| 23;\n 2 -->|output| 23;\n 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a[\"Output\\nanndata gene matrix\"];\n 23 --> 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a;\n style 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a stroke:#2c3143,stroke-width:4px;\n 24[\"scanpy_filter_genes\"];\n 23 -->|anndata_out| 24;\n 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66[\"Output\\nanndata filter genes\"];\n 24 --> 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66;\n style 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66 stroke:#2c3143,stroke-width:4px;\n 25[\"Normalize\"];\n 24 -->|anndata_out| 25;\n 7dddd4c8-1944-4f50-b331-857d03cc9631[\"Output\\nanndata normalize\"];\n 25 --> 7dddd4c8-1944-4f50-b331-857d03cc9631;\n style 7dddd4c8-1944-4f50-b331-857d03cc9631 stroke:#2c3143,stroke-width:4px;\n 26[\"pp.log1p\"];\n 25 -->|anndata_out| 26;\n 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee[\"Output\\nanndata log1p\"];\n 26 --> 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee;\n style 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee stroke:#2c3143,stroke-width:4px;\n 27[\"external.pp.magic\"];\n 26 -->|anndata_out| 27;\n 8c1c7aa9-b9dd-467b-9715-73773aea093f[\"Output\\nanndata_magic\"];\n 27 --> 8c1c7aa9-b9dd-467b-9715-73773aea093f;\n style 8c1c7aa9-b9dd-467b-9715-73773aea093f stroke:#2c3143,stroke-width:4px;\n 28[\"Copy obsm\"];\n 21 -->|anndata_out| 28;\n 27 -->|anndata_out| 28;\n 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e[\"Output\\nanndata_gene-matrix_leiden\"];\n 28 --> 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e;\n style 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e stroke:#2c3143,stroke-width:4px;\n 29[\"umap_plot_with_scanpy\"];\n 28 -->|output_h5ad| 29;\n 4 -->|output| 29;\n 4cfbbb70-156b-48d7-b14b-db21198d9b6d[\"Output\\numap_marker-genes\"];\n 29 --> 4cfbbb70-156b-48d7-b14b-db21198d9b6d;\n style 4cfbbb70-156b-48d7-b14b-db21198d9b6d stroke:#2c3143,stroke-width:4px;\n 30[\"Inspect observations\"];\n 28 -->|output_h5ad| 30;\n 31[\"Cut leiden from table\"];\n 30 -->|obs| 31;\n 11c22200-a54e-4585-82c4-8457dbbfb53c[\"Output\\nleiden annotation\"];\n 31 --> 11c22200-a54e-4585-82c4-8457dbbfb53c;\n style 11c22200-a54e-4585-82c4-8457dbbfb53c stroke:#2c3143,stroke-width:4px;\n 32[\"Replace leiden\"];\n 31 -->|out_file1| 32;\n 5 -->|output| 32;\n 467de061-79e6-4148-8a65-c06383a14012[\"Output\\ncell type annotation\"];\n 32 --> 467de061-79e6-4148-8a65-c06383a14012;\n style 467de061-79e6-4148-8a65-c06383a14012 stroke:#2c3143,stroke-width:4px;\n 33[\"Manipulate AnnData\"];\n 28 -->|output_h5ad| 33;\n 32 -->|outfile_replace| 33;\n cbba6173-f439-4fd5-8423-946aa625112b[\"Output\\nanndata_cell_type\"];\n 33 --> cbba6173-f439-4fd5-8423-946aa625112b;\n style cbba6173-f439-4fd5-8423-946aa625112b stroke:#2c3143,stroke-width:4px;\n 34[\"Plot cell types\"];\n 33 -->|anndata| 34;\n c28c53ae-8ee7-47d7-8a00-352908bb7c1a[\"Output\\numap_cell-type\"];\n 34 --> c28c53ae-8ee7-47d7-8a00-352908bb7c1a;\n style c28c53ae-8ee7-47d7-8a00-352908bb7c1a stroke:#2c3143,stroke-width:4px;\n 35[\"Final Anndata general info\"];\n 33 -->|anndata| 35;\n 379a85d1-a204-4b0b-8b33-86e5582fc51f[\"Output\\ngeneral\"];\n 35 --> 379a85d1-a204-4b0b-8b33-86e5582fc51f;\n style 379a85d1-a204-4b0b-8b33-86e5582fc51f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
"outputs": [
{
@@ -705643,30 +654491,6 @@
}
],
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.json",
- "contributions": {
- "authorship": [
- "bebatut",
- "hrhotz",
- "mtekman",
- "pavanvidem",
- "dianichj"
- ],
- "reviewing": [
- "bgruening",
- "teresa-m",
- "Nilchia",
- "shiltemann",
- "pavanvidem",
- "mtekman",
- "nomadscientist",
- "hexylena",
- "hrhotz",
- "nsoranzo",
- "mvdbeek",
- "abretaud",
- "natefoo"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -705720,285 +654544,39 @@
},
{
"affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "pavanvidem",
- "joined": "2017-09",
- "name": "Pavankumar Videm",
- "orcid": "0000-0002-5192-126X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "email": "dianachj@informatik.uni-freiburg.de",
- "id": "dianichj",
- "joined": "2024-08",
- "name": "Diana Chiang Jurado",
- "orcid": "0000-0002-5857-1477",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/dianichj.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "Nilchia",
- "joined": "2024-07",
- "name": "Amirhossein Naghsh Nilchi",
- "orcid": "0000-0003-1329-3044",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/Nilchia.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
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- "elixir-europe"
- ],
- "id": "pavanvidem",
- "joined": "2017-09",
- "name": "Pavankumar Videm",
- "orcid": "0000-0002-5192-126X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
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- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
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- ],
- "bio": "Senior Lecturer at The Open University",
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- "matrix": "nomadscientist:matrix.org",
- "name": "Wendi Bacon",
- "orcid": "0000-0002-8170-8806",
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],
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},
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],
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- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
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"questions": [
@@ -706094,16 +654672,16 @@
],
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},
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{
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"0.6.22.post1+galaxy4",
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]
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@@ -706805,6 +655366,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"1.4.4.post1+galaxy2",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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- "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy1",
"1.4+galaxy0",
- "1.4.4.post1+galaxy2"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
+ "1.4.4.post1+galaxy0"
]
},
{
@@ -707238,10 +655790,6 @@
"state": "exact",
"version": "1.10.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -707290,6 +655838,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -707342,10 +655894,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -707380,9 +655928,9 @@
"versions": [
"1.4.4+galaxy0",
"1.4.4.post1+galaxy0",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy2",
- "1.4+galaxy0"
+ "1.4.4.post1+galaxy2"
]
},
{
@@ -707397,10 +655945,6 @@
"state": "exact",
"version": "1.10.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -707449,6 +655993,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -707501,10 +656049,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -707537,11 +656081,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy2",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy0",
- "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
"1.4.4.post1+galaxy1",
- "1.4+galaxy0"
+ "1.4.4+galaxy0"
]
},
{
@@ -707556,10 +656100,6 @@
"state": "exact",
"version": "1.10.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -707608,6 +656148,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -707660,10 +656204,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -707696,10 +656236,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -707715,10 +656255,6 @@
"state": "exact",
"version": "1.10.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -707767,6 +656303,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -707819,10 +656359,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -707855,10 +656391,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "1.4.4.post1",
"1.4.4.post1+galaxy2",
"1.4.4",
"1.4.4.post1+galaxy1",
- "1.4.4.post1",
"1.4"
]
},
@@ -707874,10 +656410,6 @@
"state": "exact",
"version": "1.10.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -707943,7 +656475,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 272,
- "visitors": 2248722,
+ "visitors": 2259461,
"workflows": [
{
"creators": [
@@ -708093,7 +656625,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nMatrix\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Import Anndata\"];\n 2 -->|output| 3;\n 0 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Inspect AnnData\"];\n 3 -->|anndata| 4;\n 5[\"Scanpy filter\"];\n 3 -->|anndata| 5;\n 6[\"Inspect AnnData\"];\n 3 -->|anndata| 6;\n 7[\"Inspect AnnData\"];\n 3 -->|anndata| 7;\n 8[\"Inspect AnnData\"];\n 3 -->|anndata| 8;\n 9[\"Manipulate AnnData\"];\n 5 -->|anndata_out| 9;\n 10[\"Scanpy Inspect and manipulate\"];\n 9 -->|anndata| 10;\n 11[\"Inspect AnnData\"];\n 9 -->|anndata| 11;\n 12[\"Scanpy plot\"];\n 10 -->|anndata_out| 12;\n a13ef439-dade-4aa1-91d3-0e050da961af[\"Output\\npl_scatter_total_counts_vs_n_genes_by_counts\"];\n 12 --> a13ef439-dade-4aa1-91d3-0e050da961af;\n style a13ef439-dade-4aa1-91d3-0e050da961af stroke:#2c3143,stroke-width:4px;\n 13[\"Scanpy filter\"];\n 10 -->|anndata_out| 13;\n 14[\"Scanpy plot\"];\n 10 -->|anndata_out| 14;\n f3ed5faf-e274-4575-91d4-c6a49d1aef6d[\"Output\\npl_scatter_n_genes_by_counts_vs_pct_mito\"];\n 14 --> f3ed5faf-e274-4575-91d4-c6a49d1aef6d;\n style f3ed5faf-e274-4575-91d4-c6a49d1aef6d stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy plot\"];\n 10 -->|anndata_out| 15;\n 51634f2e-a033-4ef8-a785-079c415ccfae[\"Output\\npl_violin\"];\n 15 --> 51634f2e-a033-4ef8-a785-079c415ccfae;\n style 51634f2e-a033-4ef8-a785-079c415ccfae stroke:#2c3143,stroke-width:4px;\n 16[\"Scanpy filter\"];\n 13 -->|anndata_out| 16;\n 17[\"Manipulate AnnData\"];\n 16 -->|anndata_out| 17;\n 18[\"Scanpy normalize\"];\n 17 -->|anndata| 18;\n 19[\"Scanpy Inspect and manipulate\"];\n 18 -->|anndata_out| 19;\n 20[\"Manipulate AnnData\"];\n 19 -->|anndata_out| 20;\n 21[\"Scanpy filter\"];\n 20 -->|anndata| 21;\n 22[\"Manipulate AnnData\"];\n 21 -->|anndata_out| 22;\n 23[\"Scanpy plot\"];\n 21 -->|anndata_out| 23;\n 7c1818c2-b46f-4274-b309-68b45c7387f9[\"Output\\npl_highly_variable\"];\n 23 --> 7c1818c2-b46f-4274-b309-68b45c7387f9;\n style 7c1818c2-b46f-4274-b309-68b45c7387f9 stroke:#2c3143,stroke-width:4px;\n 24[\"Scanpy remove confounders\"];\n 22 -->|anndata| 24;\n 25[\"Scanpy Inspect and manipulate\"];\n 24 -->|anndata_out| 25;\n 26[\"Scanpy cluster, embed\"];\n 25 -->|anndata_out| 26;\n 27[\"Scanpy plot\"];\n 26 -->|anndata_out| 27;\n 9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3[\"Output\\npl_pca_overview\"];\n 27 --> 9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3;\n style 9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3 stroke:#2c3143,stroke-width:4px;\n 28[\"Scanpy plot\"];\n 26 -->|anndata_out| 28;\n 23fad9ca-caed-4cb5-bf9c-77dccd7fff09[\"Output\\npl_pca_overview_genes\"];\n 28 --> 23fad9ca-caed-4cb5-bf9c-77dccd7fff09;\n style 23fad9ca-caed-4cb5-bf9c-77dccd7fff09 stroke:#2c3143,stroke-width:4px;\n 29[\"Scanpy plot\"];\n 26 -->|anndata_out| 29;\n d80530df-fb7b-4d72-8c12-ae09d9eccc7c[\"Output\\npl_pca_loadings\"];\n 29 --> d80530df-fb7b-4d72-8c12-ae09d9eccc7c;\n style d80530df-fb7b-4d72-8c12-ae09d9eccc7c stroke:#2c3143,stroke-width:4px;\n 30[\"Scanpy Inspect and manipulate\"];\n 26 -->|anndata_out| 30;\n 31[\"Scanpy plot\"];\n 26 -->|anndata_out| 31;\n 2e3480a4-1dfb-4e43-b70c-459d155853e9[\"Output\\npl_pca_variance_ratio\"];\n 31 --> 2e3480a4-1dfb-4e43-b70c-459d155853e9;\n style 2e3480a4-1dfb-4e43-b70c-459d155853e9 stroke:#2c3143,stroke-width:4px;\n 32[\"Scanpy cluster, embed\"];\n 30 -->|anndata_out| 32;\n 33[\"Scanpy plot\"];\n 32 -->|anndata_out| 33;\n 504ea6ab-68a6-4c37-ae97-c58a99ff8381[\"Output\\npl_umap_initial\"];\n 33 --> 504ea6ab-68a6-4c37-ae97-c58a99ff8381;\n style 504ea6ab-68a6-4c37-ae97-c58a99ff8381 stroke:#2c3143,stroke-width:4px;\n 34[\"Scanpy cluster, embed\"];\n 32 -->|anndata_out| 34;\n 35[\"Scanpy plot\"];\n 34 -->|anndata_out| 35;\n c674ba29-f097-4242-8dc2-b22441233e73[\"Output\\npl_umap_louvain\"];\n 35 --> c674ba29-f097-4242-8dc2-b22441233e73;\n style c674ba29-f097-4242-8dc2-b22441233e73 stroke:#2c3143,stroke-width:4px;\n 36[\"Scanpy Inspect and manipulate\"];\n 34 -->|anndata_out| 36;\n 37[\"Scanpy Inspect and manipulate\"];\n 34 -->|anndata_out| 37;\n 38[\"Inspect clusters\"];\n 36 -->|anndata_out| 38;\n 39[\"Scanpy plot\"];\n 36 -->|anndata_out| 39;\n 249d7c38-140c-403d-a0ed-effe1a17fdd6[\"Output\\npl_rank_gene_groups_t_test_wilcoxon_test\"];\n 39 --> 249d7c38-140c-403d-a0ed-effe1a17fdd6;\n style 249d7c38-140c-403d-a0ed-effe1a17fdd6 stroke:#2c3143,stroke-width:4px;\n 40[\"Scanpy plot\"];\n 36 -->|anndata_out| 40;\n c1395d95-9c53-48c9-972e-cf93116e85db[\"Output\\npl_rank_genes_heatmap\"];\n 40 --> c1395d95-9c53-48c9-972e-cf93116e85db;\n style c1395d95-9c53-48c9-972e-cf93116e85db stroke:#2c3143,stroke-width:4px;\n 41[\"Scanpy plot\"];\n 36 -->|anndata_out| 41;\n 6b30a9d8-01be-4757-999d-cade6b516df6[\"Output\\npl_stacked_violin_marker_genes\"];\n 41 --> 6b30a9d8-01be-4757-999d-cade6b516df6;\n style 6b30a9d8-01be-4757-999d-cade6b516df6 stroke:#2c3143,stroke-width:4px;\n 42[\"Scanpy plot\"];\n 36 -->|anndata_out| 42;\n 30bc8ca7-37b7-4efc-b442-8bc4cb986d7e[\"Output\\npl_umap_marker_genes\"];\n 42 --> 30bc8ca7-37b7-4efc-b442-8bc4cb986d7e;\n style 30bc8ca7-37b7-4efc-b442-8bc4cb986d7e stroke:#2c3143,stroke-width:4px;\n 43[\"Scanpy Inspect and manipulate\"];\n 36 -->|anndata_out| 43;\n 44[\"Inspect AnnData\"];\n 36 -->|anndata_out| 44;\n 9092ecc8-cace-45c4-8efa-bd4d27275060[\"Output\\nuns_rank_genes_groups_names_wilcoxon_test\"];\n 44 --> 9092ecc8-cace-45c4-8efa-bd4d27275060;\n style 9092ecc8-cace-45c4-8efa-bd4d27275060 stroke:#2c3143,stroke-width:4px;\n 45[\"Manipulate AnnData\"];\n 36 -->|anndata_out| 45;\n 545a105c-1202-4209-aff2-201fd953e398[\"Output\\nanndata_out\"];\n 45 --> 545a105c-1202-4209-aff2-201fd953e398;\n style 545a105c-1202-4209-aff2-201fd953e398 stroke:#2c3143,stroke-width:4px;\n 46[\"Scanpy plot\"];\n 36 -->|anndata_out| 46;\n ad91827e-e8cc-45ec-b32f-935cf44a77d1[\"Output\\npl_violin_louvain\"];\n 46 --> ad91827e-e8cc-45ec-b32f-935cf44a77d1;\n style ad91827e-e8cc-45ec-b32f-935cf44a77d1 stroke:#2c3143,stroke-width:4px;\n 47[\"Scanpy plot\"];\n 37 -->|anndata_out| 47;\n 4011556e-85f9-470e-b902-7ef9df11fef5[\"Output\\npl_rank_gene_groups_t_test\"];\n 47 --> 4011556e-85f9-470e-b902-7ef9df11fef5;\n style 4011556e-85f9-470e-b902-7ef9df11fef5 stroke:#2c3143,stroke-width:4px;\n 48[\"Inspect AnnData\"];\n 37 -->|anndata_out| 48;\n 55f664c3-b771-4115-890f-3eb4637813b0[\"Output\\nuns_rank_genes_groups_names_t_test\"];\n 48 --> 55f664c3-b771-4115-890f-3eb4637813b0;\n style 55f664c3-b771-4115-890f-3eb4637813b0 stroke:#2c3143,stroke-width:4px;\n 49[\"Datamash\"];\n 38 -->|obs| 49;\n 10693ba5-026d-443b-aa80-b4dedbf4f940[\"Output\\ncells_per_cluster\"];\n 49 --> 10693ba5-026d-443b-aa80-b4dedbf4f940;\n style 10693ba5-026d-443b-aa80-b4dedbf4f940 stroke:#2c3143,stroke-width:4px;\n 50[\"Scanpy plot\"];\n 43 -->|anndata_out| 50;\n 51878bf2-d055-4acc-b365-cc7f7a673f66[\"Output\\npl_rank_gene_groups_0_vs_1\"];\n 50 --> 51878bf2-d055-4acc-b365-cc7f7a673f66;\n style 51878bf2-d055-4acc-b365-cc7f7a673f66 stroke:#2c3143,stroke-width:4px;\n 51[\"Scanpy plot\"];\n 43 -->|anndata_out| 51;\n 10a46aa1-5685-4480-a6eb-362f32b91fa1[\"Output\\npl_rank_gene_groups_violin_0_vs_1\"];\n 51 --> 10a46aa1-5685-4480-a6eb-362f32b91fa1;\n style 10a46aa1-5685-4480-a6eb-362f32b91fa1 stroke:#2c3143,stroke-width:4px;\n 52[\"Scanpy plot\"];\n 45 -->|anndata| 52;\n c8ae2d77-361a-41e0-b238-0f494d12b6d7[\"Output\\npl_umap_celltypes\"];\n 52 --> c8ae2d77-361a-41e0-b238-0f494d12b6d7;\n style c8ae2d77-361a-41e0-b238-0f494d12b6d7 stroke:#2c3143,stroke-width:4px;\n 53[\"Scanpy plot\"];\n 45 -->|anndata| 53;\n a3ceb616-64b8-4c79-ba94-4272a5bd747f[\"Output\\npl_dotplot_marker_genes\"];\n 53 --> a3ceb616-64b8-4c79-ba94-4272a5bd747f;\n style a3ceb616-64b8-4c79-ba94-4272a5bd747f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Clustering 3k PBMC with Scanpy",
"outputs": [
{
@@ -709540,7 +658072,7 @@
"Appraise data outputs and decisions",
"Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
],
- "pageviews": 2607,
+ "pageviews": 2637,
"priority": 2,
"pub_date": "2023-08-25",
"questions": [
@@ -709645,7 +658177,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 96,
- "visitors": 2193,
+ "visitors": 2218,
"zenodo_link": "https://zenodo.org/record/7053673"
},
{
@@ -709679,21 +658211,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n owner: iuc\n revisions: 6a675c3aa610\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seq_filter_by_id\n owner: peterjc\n revisions: 141612f8c3e3\n tool_panel_section_label: Filter and Sort\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json",
- "contributions": {
- "authorship": [
- "mtekman"
- ],
- "reviewing": [
- "mtekman",
- "lldelisle",
- "hexylena",
- "shiltemann",
- "nsoranzo",
- "bebatut",
- "bgruening",
- "nomadscientist"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -709709,202 +658226,13 @@
"name": "Mehmet Tekman",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
- "id": "mtekman",
- "joined": "2018-11",
- "name": "Mehmet Tekman",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "ch",
- "email": "lucille.delisle@epfl.ch",
- "id": "lldelisle",
- "joined": "2019-08",
- "location": {
- "country": "CH",
- "lat": 46.52,
- "lon": 6.56
- },
- "name": "Lucille Delisle",
- "orcid": "0000-0002-1964-4960",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "earlham",
- "elixir-europe"
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}
],
"dir": "topics/single-cell/tutorials/scrna-umis",
"edam_operation": [
+ "Sequencing quality control",
"Sequence composition calculation",
- "Statistical calculation",
- "Sequencing quality control"
+ "Statistical calculation"
],
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"exact_supported_servers": [
@@ -709919,8 +658247,7 @@
"hands_on": true,
"id": "single-cell/scrna-umis",
"inexact_supported_servers": [
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- "UseGalaxy.fr"
+ "UseGalaxy.cz"
],
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@@ -709938,7 +658265,7 @@
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"Understand and validate the extraction of barcodes"
],
- "pageviews": 6475,
+ "pageviews": 6493,
"priority": 2,
"pub_date": "2019-02-20",
"questions": [
@@ -709967,9 +658294,9 @@
],
"short_id": "T00256",
"short_tools": [
- "umi_tools_extract",
+ "seq_filter_by_id",
"fastqc",
- "seq_filter_by_id"
+ "umi_tools_extract"
],
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"slides_recordings": false,
@@ -710002,11 +658329,6 @@
"name": "UseGalaxy.cz",
"url": "https://usegalaxy.cz/",
"usegalaxy": false
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- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -710032,6 +658354,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -710087,10 +658413,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -710137,11 +658459,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -710186,6 +658503,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -710243,10 +658564,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"0.68",
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"0.64",
"0.62"
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{
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"state": "exact",
@@ -710360,6 +658672,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -710412,10 +658728,6 @@
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{
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@@ -710449,178 +658761,164 @@
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- {
- "server": "https://usegalaxy.be/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "0.5.3.2"
+ ]
},
{
"server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "1.1.2+galaxy2"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.5.5.1"
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+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
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+ "server": "https://usegalaxy.org",
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+ "state": "exact",
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
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+ "state": "missing"
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+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
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+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
"state": "exact",
"version": "0.2.7"
},
{
- "server": "https://usegalaxy.eu",
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ {
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
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+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
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+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.be/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
"state": "exact",
"version": "0.2.7"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.2.7"
},
@@ -710676,8 +658974,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 72,
- "visitors": 5140,
+ "visit_duration": 71,
+ "visitors": 5156,
"zenodo_link": "https://zenodo.org/record/2573177"
},
{
@@ -711008,7 +659306,6 @@
"edam_topic": [],
"exact_supported_servers": [
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- "UseGalaxy.fr",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
],
@@ -711037,7 +659334,7 @@
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],
- "pageviews": 988,
+ "pageviews": 1020,
"priority": 3,
"pub_date": "2024-04-09",
"questions": [
@@ -711057,18 +659354,18 @@
],
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"short_tools": [
- "seurat_read10x",
- "seurat_run_pca",
- "seurat_scale_data",
- "retrieve_scxa",
- "seurat_filter_cells",
+ "seurat_find_markers",
"seurat_plot",
- "seurat_find_clusters",
"seurat_run_umap",
"seurat_normalise_data",
"seurat_find_neighbours",
"seurat_find_variable_genes",
- "seurat_find_markers"
+ "seurat_run_pca",
+ "retrieve_scxa",
+ "seurat_scale_data",
+ "seurat_filter_cells",
+ "seurat_read10x",
+ "seurat_find_clusters"
],
"slides": false,
"slides_recordings": false,
@@ -711080,11 +659377,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -711120,6 +659412,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -711175,10 +659471,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -711225,11 +659517,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -711274,6 +659561,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -711326,10 +659617,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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@@ -711372,11 +659659,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
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- "version": "v0.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -711422,6 +659704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -711474,10 +659760,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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{
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"state": "exact",
@@ -711520,11 +659802,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -711569,6 +659846,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -711621,10 +659902,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "exact",
@@ -711667,11 +659944,6 @@
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},
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- "version": "4.0.4+galaxy0"
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{
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"state": "missing"
@@ -711716,6 +659988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -711768,10 +660044,6 @@
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@@ -711863,6 +660130,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -712010,6 +660272,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -712157,6 +660414,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -712255,11 +660512,6 @@
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"state": "missing"
@@ -712304,6 +660556,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -712356,10 +660612,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -712402,11 +660654,6 @@
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- "state": "exact",
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- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -712451,6 +660698,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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- "state": "missing"
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{
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"state": "exact",
@@ -712549,11 +660796,6 @@
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},
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- "version": "4.0.4+galaxy0"
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{
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"state": "missing"
@@ -712598,6 +660840,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -712650,10 +660896,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -712696,11 +660938,6 @@
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},
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- "state": "exact",
- "version": "4.0.4+galaxy0"
- },
{
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"state": "missing"
@@ -712745,6 +660982,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -712797,10 +661038,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -712843,11 +661080,6 @@
"state": "exact",
"version": "4.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -712892,6 +661124,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -712944,10 +661180,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -712990,11 +661222,6 @@
"state": "exact",
"version": "4.0.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -713059,8 +661286,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 74,
- "visitors": 794,
+ "visit_duration": 72,
+ "visitors": 821,
"workflows": [
{
"creators": [
@@ -713102,7 +661329,7 @@
"inputs": [],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"EBI SCXA Data Retrieval\"];\n a5a4504c-013b-4b87-8ef2-643a3e1804bb[\"Output\\nmatrix_mtx\"];\n 0 --> a5a4504c-013b-4b87-8ef2-643a3e1804bb;\n style a5a4504c-013b-4b87-8ef2-643a3e1804bb stroke:#2c3143,stroke-width:4px;\n b4ce8ebe-421f-4259-b822-3ac79c5f9817[\"Output\\ngenes_tsv\"];\n 0 --> b4ce8ebe-421f-4259-b822-3ac79c5f9817;\n style b4ce8ebe-421f-4259-b822-3ac79c5f9817 stroke:#2c3143,stroke-width:4px;\n 83aed959-6dce-4115-86dd-7b2d2eeceb00[\"Output\\ndesign_tsv\"];\n 0 --> 83aed959-6dce-4115-86dd-7b2d2eeceb00;\n style 83aed959-6dce-4115-86dd-7b2d2eeceb00 stroke:#2c3143,stroke-width:4px;\n ca12560b-ca83-4447-8096-acbd51760079[\"Output\\nbarcode_tsv\"];\n 0 --> ca12560b-ca83-4447-8096-acbd51760079;\n style ca12560b-ca83-4447-8096-acbd51760079 stroke:#2c3143,stroke-width:4px;\n 1[\"Seurat Read10x\"];\n 0 -->|barcode_tsv| 1;\n 0 -->|genes_tsv| 1;\n 0 -->|matrix_mtx| 1;\n 0 -->|design_tsv| 1;\n 2[\"Plot\"];\n 1 -->|rds_seurat_file| 2;\n 3[\"Seurat FilterCells\"];\n 1 -->|rds_seurat_file| 3;\n 4[\"Seurat NormaliseData\"];\n 3 -->|rds_seurat_file| 4;\n 5[\"Seurat FindVariableGenes\"];\n 4 -->|rds_seurat_file| 5;\n 6[\"Seurat ScaleData\"];\n 5 -->|output_tab| 6;\n 5 -->|rds_seurat_file| 6;\n 7[\"Seurat RunPCA\"];\n 6 -->|rds_seurat_file| 7;\n 5 -->|output_tab| 7;\n 8[\"Seurat FindNeighbours\"];\n 7 -->|rds_seurat_file| 8;\n 9[\"Seurat FindClusters\"];\n 8 -->|rds_seurat_file| 9;\n ac5e668c-341b-4887-867c-0ba165d2a874[\"Output\\nrds_seurat_clusters\"];\n 9 --> ac5e668c-341b-4887-867c-0ba165d2a874;\n style ac5e668c-341b-4887-867c-0ba165d2a874 stroke:#2c3143,stroke-width:4px;\n 10[\"Seurat UMAP\"];\n 9 -->|rds_seurat_file| 10;\n 831e32ad-773b-417c-8b7e-4b7ca0e12488[\"Output\\nrds_seurat_umap\"];\n 10 --> 831e32ad-773b-417c-8b7e-4b7ca0e12488;\n style 831e32ad-773b-417c-8b7e-4b7ca0e12488 stroke:#2c3143,stroke-width:4px;\n 11[\"Plot\"];\n 10 -->|rds_seurat_file| 11;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Seurat Filter, Plot and Exlore tutorial",
"outputs": [
{
@@ -713307,7 +661534,7 @@
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0",
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0"
],
- "workflowhub_id": null
+ "workflowhub_id": "1375"
}
],
"zenodo_link": "https://zenodo.org/record/7053673"
@@ -713882,7 +662109,7 @@
"Appraise data outputs and decisions",
"Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
],
- "pageviews": 6840,
+ "pageviews": 6916,
"priority": 3,
"pub_date": "2021-03-24",
"questions": [
@@ -713922,25 +662149,25 @@
],
"short_id": "T00247",
"short_tools": [
+ "Cut1",
"scanpy_find_markers",
- "scanpy_run_pca",
- "scanpy_find_variable_genes",
"anndata_ops",
- "scanpy_filter_cells",
- "scanpy_plot_embed",
"interactive_tool_cellxgene",
- "scanpy_compute_graph",
- "scanpy_run_tsne",
"scanpy_find_cluster",
- "join1",
- "Cut1",
- "scanpy_plot",
+ "scanpy_compute_graph",
+ "scanpy_filter_genes",
+ "scanpy_find_variable_genes",
+ "scanpy_scale_data",
"scanpy_normalise_data",
+ "anndata_manipulate",
+ "scanpy_plot",
+ "scanpy_filter_cells",
+ "scanpy_plot_embed",
+ "join1",
"scanpy_run_umap",
"anndata_inspect",
- "anndata_manipulate",
- "scanpy_scale_data",
- "scanpy_filter_genes"
+ "scanpy_run_tsne",
+ "scanpy_run_pca"
],
"slides": false,
"slides_recordings": false,
@@ -713982,6 +662209,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -714037,10 +662268,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -714087,11 +662314,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -714136,6 +662358,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -714188,10 +662414,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -714232,10 +662454,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -714278,6 +662496,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -714330,10 +662552,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -714374,10 +662592,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -714420,6 +662634,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -714472,10 +662690,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -714516,10 +662730,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -714562,6 +662772,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -714614,10 +662828,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -714659,10 +662869,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -714672,9 +662878,9 @@
"state": "inexact",
"versions": [
"1.8.1+galaxy9",
+ "1.7.2+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0",
- "1.7.2+galaxy0"
+ "1.8.1+2+galaxy0"
]
},
{
@@ -714712,6 +662918,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -714764,10 +662974,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -714809,10 +663015,6 @@
"state": "exact",
"version": "1.8.1+galaxy91"
},
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -714822,9 +663024,9 @@
"state": "inexact",
"versions": [
"1.8.1+galaxy9",
+ "1.7.2+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0",
- "1.7.2+galaxy0"
+ "1.8.1+2+galaxy0"
]
},
{
@@ -714862,6 +663064,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -714914,10 +663120,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -714962,10 +663164,6 @@
"state": "exact",
"version": "1.8.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -714977,11 +663175,11 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.8.1+galaxy9",
- "1.9.3+galaxy0",
"1.6.0+galaxy3",
+ "1.7.2+galaxy1",
+ "1.9.3+galaxy0",
"1.8.1+2+galaxy0",
- "1.7.2+galaxy1"
+ "1.8.1+galaxy9"
]
},
{
@@ -715019,6 +663217,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715071,10 +663273,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715119,10 +663317,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715170,6 +663364,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715222,10 +663420,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715270,10 +663464,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715285,11 +663475,11 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.7.2+galaxy0",
+ "1.6.0+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0",
+ "1.7.2+galaxy0",
"1.8.1+galaxy9",
- "1.6.0+galaxy0"
+ "1.8.1+2+galaxy0"
]
},
{
@@ -715327,6 +663517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715379,10 +663573,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715427,10 +663617,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715478,6 +663664,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715530,10 +663720,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715578,10 +663764,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715593,11 +663775,11 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
+ "1.9.3+galaxy0",
"1.8.1+galaxy9",
+ "1.8.1+2+galaxy0",
"1.6.0+galaxy0",
- "1.7.2+galaxy0",
- "1.9.3+galaxy0",
- "1.8.1+2+galaxy0"
+ "1.7.2+galaxy0"
]
},
{
@@ -715635,6 +663817,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715687,10 +663873,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715735,10 +663917,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715786,6 +663964,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715838,10 +664020,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -715886,10 +664064,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -715901,10 +664075,10 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.8.1+2+galaxy0",
+ "1.8.1+galaxy9",
"1.7.2+galaxy0",
+ "1.8.1+2+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+galaxy9",
"1.6.0+galaxy3"
]
},
@@ -715943,6 +664117,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -715995,10 +664173,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716043,10 +664217,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716094,6 +664264,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716146,10 +664320,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716194,10 +664364,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716210,9 +664376,9 @@
"state": "inexact",
"versions": [
"1.6.0+galaxy4",
- "1.7.2+galaxy0",
"1.8.1+galaxy9",
"1.8.1+2+galaxy1",
+ "1.7.2+galaxy0",
"1.9.3+galaxy0"
]
},
@@ -716251,6 +664417,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716303,10 +664473,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716351,10 +664517,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716402,6 +664564,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716454,10 +664620,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716502,10 +664664,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716559,6 +664717,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716611,10 +664773,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716659,10 +664817,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716710,6 +664864,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716762,10 +664920,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716810,10 +664964,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -716825,10 +664975,10 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.7.2+galaxy0",
+ "1.8.1+2+galaxy0",
"1.8.1+galaxy9",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0"
+ "1.7.2+galaxy0"
]
},
{
@@ -716866,6 +665016,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -716918,10 +665072,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -716966,10 +665116,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -717017,6 +665163,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717069,10 +665219,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717114,10 +665260,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -717126,8 +665268,8 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.8.1+2+galaxy0",
"1.8.1+galaxy9",
+ "1.8.1+2+galaxy0",
"1.7.2+galaxy0",
"1.9.3+galaxy0"
]
@@ -717167,6 +665309,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717219,10 +665365,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717264,10 +665406,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -717312,6 +665450,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717364,10 +665506,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717412,10 +665550,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -717427,11 +665561,11 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.6.0+galaxy1",
- "1.8.1+galaxy9",
"1.7.2+galaxy0",
+ "1.6.0+galaxy1",
"1.9.3+galaxy0",
- "1.8.1+2+galaxy0"
+ "1.8.1+2+galaxy0",
+ "1.8.1+galaxy9"
]
},
{
@@ -717469,6 +665603,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717521,10 +665659,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717569,10 +665703,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -717620,6 +665750,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717672,10 +665806,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717720,10 +665850,6 @@
"state": "exact",
"version": "1.8.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -717735,11 +665861,11 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
+ "1.7.2+galaxy0",
+ "1.6.0+galaxy2",
"1.9.3+galaxy0",
"1.8.1+galaxy9",
- "1.7.2+galaxy0",
- "1.8.1+2+galaxy0",
- "1.6.0+galaxy2"
+ "1.8.1+2+galaxy0"
]
},
{
@@ -717777,6 +665903,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717829,10 +665959,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -717877,10 +666003,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -717928,6 +666050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -717980,10 +666106,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718028,10 +666150,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -718045,8 +666163,8 @@
"versions": [
"1.8.1+2+galaxy0",
"1.8.1+galaxy9",
- "1.6.0+galaxy1",
"1.9.3+galaxy0",
+ "1.6.0+galaxy1",
"1.7.2+galaxy0"
]
},
@@ -718085,6 +666203,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718137,10 +666259,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718185,10 +666303,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -718236,6 +666350,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718288,10 +666406,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718336,10 +666450,6 @@
"state": "exact",
"version": "1.8.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -718351,10 +666461,10 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.7.2+galaxy0",
"1.8.1+2+galaxy0",
- "1.8.1+galaxy9"
+ "1.8.1+galaxy9",
+ "1.9.3+galaxy0",
+ "1.7.2+galaxy0"
]
},
{
@@ -718392,6 +666502,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718444,10 +666558,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718492,10 +666602,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -718543,6 +666649,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718595,10 +666705,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718632,10 +666738,10 @@
"state": "inexact",
"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -718649,10 +666755,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -718698,6 +666800,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718750,10 +666856,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718786,10 +666888,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -718803,10 +666905,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -718852,6 +666950,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -718904,10 +667006,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -718940,10 +667038,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -718957,10 +667055,6 @@
"state": "exact",
"version": "1.7.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -719046,8 +667140,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 160,
- "visitors": 4331,
+ "visit_duration": 162,
+ "visitors": 4372,
"workflows": [
{
"creators": [],
@@ -719098,7 +667192,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Inspect AnnData\"];\n 0 -->|output| 1;\n 2[\"Scanpy FilterCells\"];\n 0 -->|output| 2;\n 08175d7f-f4f4-413c-ad86-f59587ff692e[\"Output\\nGenes-filtered Object\"];\n 2 --> 08175d7f-f4f4-413c-ad86-f59587ff692e;\n style 08175d7f-f4f4-413c-ad86-f59587ff692e stroke:#2c3143,stroke-width:4px;\n 3[\"Plot\"];\n 0 -->|output| 3;\n bfc499ee-630a-498b-9be6-696d9bb78837[\"Output\\nScatter - genes x UMIs\"];\n 3 --> bfc499ee-630a-498b-9be6-696d9bb78837;\n style bfc499ee-630a-498b-9be6-696d9bb78837 stroke:#2c3143,stroke-width:4px;\n 4[\"Plot\"];\n 0 -->|output| 4;\n f2c78ef3-7d31-4930-954c-0133cce27a41[\"Output\\nScatter - mito x genes\"];\n 4 --> f2c78ef3-7d31-4930-954c-0133cce27a41;\n style f2c78ef3-7d31-4930-954c-0133cce27a41 stroke:#2c3143,stroke-width:4px;\n 5[\"Plot\"];\n 0 -->|output| 5;\n 348818e6-9def-41fd-a390-6f8525c57cd8[\"Output\\nViolin - genotype - log\"];\n 5 --> 348818e6-9def-41fd-a390-6f8525c57cd8;\n style 348818e6-9def-41fd-a390-6f8525c57cd8 stroke:#2c3143,stroke-width:4px;\n 6[\"Plot\"];\n 0 -->|output| 6;\n 844f5e7c-78c8-4f28-8e15-cea35ada8fef[\"Output\\nViolin - batch - log\"];\n 6 --> 844f5e7c-78c8-4f28-8e15-cea35ada8fef;\n style 844f5e7c-78c8-4f28-8e15-cea35ada8fef stroke:#2c3143,stroke-width:4px;\n 7[\"Inspect AnnData\"];\n 0 -->|output| 7;\n 8[\"Plot\"];\n 0 -->|output| 8;\n 3b1232c5-d16a-434d-806e-79fd77f7c05f[\"Output\\nScatter - mito x UMIs\"];\n 8 --> 3b1232c5-d16a-434d-806e-79fd77f7c05f;\n style 3b1232c5-d16a-434d-806e-79fd77f7c05f stroke:#2c3143,stroke-width:4px;\n 9[\"Inspect AnnData\"];\n 0 -->|output| 9;\n 10[\"Plot\"];\n 0 -->|output| 10;\n a639cdc0-da40-4df9-8348-23117528b24a[\"Output\\nViolin - sex - log\"];\n 10 --> a639cdc0-da40-4df9-8348-23117528b24a;\n style a639cdc0-da40-4df9-8348-23117528b24a stroke:#2c3143,stroke-width:4px;\n 11[\"Plot\"];\n 2 -->|output_h5ad| 11;\n 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691[\"Output\\nViolin - Filterbygenes\"];\n 11 --> 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691;\n style 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691 stroke:#2c3143,stroke-width:4px;\n 12[\"Scanpy FilterCells\"];\n 2 -->|output_h5ad| 12;\n f378cb4e-0a77-49d9-b92a-752dbea4b09a[\"Output\\nCounts-filtered Object\"];\n 12 --> f378cb4e-0a77-49d9-b92a-752dbea4b09a;\n style f378cb4e-0a77-49d9-b92a-752dbea4b09a stroke:#2c3143,stroke-width:4px;\n 13[\"Inspect AnnData\"];\n 2 -->|output_h5ad| 13;\n f9e862db-eb22-4124-8fe0-0fdcfcfb8393[\"Output\\nGeneral - Filterbygenes\"];\n 13 --> f9e862db-eb22-4124-8fe0-0fdcfcfb8393;\n style f9e862db-eb22-4124-8fe0-0fdcfcfb8393 stroke:#2c3143,stroke-width:4px;\n 14[\"Inspect AnnData\"];\n 12 -->|output_h5ad| 14;\n 794f72b5-c2c3-46a0-ac15-b9f1e94941d2[\"Output\\nGeneral - Filterbycounts\"];\n 14 --> 794f72b5-c2c3-46a0-ac15-b9f1e94941d2;\n style 794f72b5-c2c3-46a0-ac15-b9f1e94941d2 stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy FilterCells\"];\n 12 -->|output_h5ad| 15;\n b915da66-6435-4871-baa0-3e494ba73c96[\"Output\\nMito-filtered Object\"];\n 15 --> b915da66-6435-4871-baa0-3e494ba73c96;\n style b915da66-6435-4871-baa0-3e494ba73c96 stroke:#2c3143,stroke-width:4px;\n 16[\"Plot\"];\n 12 -->|output_h5ad| 16;\n 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa[\"Output\\nViolin - Filterbycounts\"];\n 16 --> 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa;\n style 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa stroke:#2c3143,stroke-width:4px;\n 17[\"Inspect AnnData\"];\n 15 -->|output_h5ad| 17;\n cd94a4c6-5665-4bdf-88ea-4f4d41efa893[\"Output\\nGeneral - Filterbymito\"];\n 17 --> cd94a4c6-5665-4bdf-88ea-4f4d41efa893;\n style cd94a4c6-5665-4bdf-88ea-4f4d41efa893 stroke:#2c3143,stroke-width:4px;\n 18[\"Scanpy FilterGenes\"];\n 15 -->|output_h5ad| 18;\n ee63ef0a-98ed-45cb-b144-1154f84ae452[\"Output\\nFiltered Object\"];\n 18 --> ee63ef0a-98ed-45cb-b144-1154f84ae452;\n style ee63ef0a-98ed-45cb-b144-1154f84ae452 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot\"];\n 15 -->|output_h5ad| 19;\n 7e48a14f-08fd-45ab-b613-606bf64dcf9d[\"Output\\nViolin - Filterbymito\"];\n 19 --> 7e48a14f-08fd-45ab-b613-606bf64dcf9d;\n style 7e48a14f-08fd-45ab-b613-606bf64dcf9d stroke:#2c3143,stroke-width:4px;\n 20[\"Inspect AnnData\"];\n 18 -->|output_h5ad| 20;\n d59efa9b-d049-4f0e-8bd8-8ae982a45d0a[\"Output\\nGeneral - Filtered object\"];\n 20 --> d59efa9b-d049-4f0e-8bd8-8ae982a45d0a;\n style d59efa9b-d049-4f0e-8bd8-8ae982a45d0a stroke:#2c3143,stroke-width:4px;\n 21[\"Scanpy NormaliseData\"];\n 18 -->|output_h5ad| 21;\n 22[\"Scanpy FindVariableGenes\"];\n 21 -->|output_h5ad| 22;\n 23[\"Scanpy ScaleData\"];\n 22 -->|output_h5ad| 23;\n 24[\"Scanpy RunPCA\"];\n 23 -->|output_h5ad| 24;\n 25[\"Plot\"];\n 24 -->|output_h5ad| 25;\n 993dea99-990f-460a-beb9-46e5c97ee898[\"Output\\nPCA Variance\"];\n 25 --> 993dea99-990f-460a-beb9-46e5c97ee898;\n style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px;\n 26[\"Scanpy ComputeGraph\"];\n 24 -->|output_h5ad| 26;\n 27[\"Scanpy RunTSNE\"];\n 26 -->|output_h5ad| 27;\n 28[\"Scanpy RunUMAP\"];\n 27 -->|output_h5ad| 28;\n 29[\"Scanpy FindCluster\"];\n 28 -->|output_h5ad| 29;\n 30[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 30;\n 308b4961-4d50-442b-9bca-bbb1992426ba[\"Output\\nMarkers - cluster\"];\n 30 --> 308b4961-4d50-442b-9bca-bbb1992426ba;\n style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px;\n 035bbbce-fb57-48c8-83d5-2b0cd0376541[\"Output\\nFinal object\"];\n 30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541;\n style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px;\n 31[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 31;\n 1705e219-192a-4f52-9b26-64fcbcd303ea[\"Output\\nMarkers - genotype\"];\n 31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea;\n style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px;\n 32[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 32;\n 33[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 33;\n 34[\"Manipulate AnnData\"];\n 30 -->|output_h5ad| 34;\n 35[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 35;\n 36[\"Inspect AnnData\"];\n 30 -->|output_h5ad| 36;\n 37[\"AnnData Operations\"];\n 34 -->|anndata| 37;\n 30 -->|output_h5ad| 37;\n 38[\"Join two Datasets\"];\n 30 -->|output_tsv| 38;\n 36 -->|var| 38;\n 39[\"Join two Datasets\"];\n 31 -->|output_tsv| 39;\n 36 -->|var| 39;\n 40[\"AnnData Operations\"];\n 37 -->|output_h5ad| 40;\n a6d48df0-403f-4efc-a75f-9504a960884e[\"Output\\nFinal cell annotated object\"];\n 40 --> a6d48df0-403f-4efc-a75f-9504a960884e;\n style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px;\n 41[\"Cut\"];\n 38 -->|out_file1| 41;\n 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9[\"Output\\nMarkers - cluster - named\"];\n 41 --> 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9;\n style 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9 stroke:#2c3143,stroke-width:4px;\n 42[\"Cut\"];\n 39 -->|out_file1| 42;\n fdb88faa-9b76-4edb-b89b-427c098a473e[\"Output\\nMarkers - genotype - named\"];\n 42 --> fdb88faa-9b76-4edb-b89b-427c098a473e;\n style fdb88faa-9b76-4edb-b89b-427c098a473e stroke:#2c3143,stroke-width:4px;\n 43[\"Scanpy PlotEmbed\"];\n 40 -->|output_h5ad| 43;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
"outputs": [
{
@@ -721345,7 +669439,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"Inspect AnnData\"];\n 0 -->|output| 1;\n 2[\"Scanpy FilterCells\"];\n 0 -->|output| 2;\n 6a00b14b-d3f8-4771-963a-76115c8eaf2f[\"Output\\nGenes-filtered Object\"];\n 2 --> 6a00b14b-d3f8-4771-963a-76115c8eaf2f;\n style 6a00b14b-d3f8-4771-963a-76115c8eaf2f stroke:#2c3143,stroke-width:4px;\n 3[\"Plot\"];\n 0 -->|output| 3;\n c123842e-b2d2-43ad-81f0-6ba3b45d4021[\"Output\\nScatter - genes x UMIs\"];\n 3 --> c123842e-b2d2-43ad-81f0-6ba3b45d4021;\n style c123842e-b2d2-43ad-81f0-6ba3b45d4021 stroke:#2c3143,stroke-width:4px;\n 4[\"Plot\"];\n 0 -->|output| 4;\n f1020d4d-555e-42fa-ba21-52a151b91a5b[\"Output\\nScatter - mito x genes\"];\n 4 --> f1020d4d-555e-42fa-ba21-52a151b91a5b;\n style f1020d4d-555e-42fa-ba21-52a151b91a5b stroke:#2c3143,stroke-width:4px;\n 5[\"Plot\"];\n 0 -->|output| 5;\n a7fe6020-8f1e-470a-9ed3-f2b5e95516e0[\"Output\\nViolin - genotype - log\"];\n 5 --> a7fe6020-8f1e-470a-9ed3-f2b5e95516e0;\n style a7fe6020-8f1e-470a-9ed3-f2b5e95516e0 stroke:#2c3143,stroke-width:4px;\n 6[\"Plot\"];\n 0 -->|output| 6;\n 15e501bc-8ddb-4519-89eb-dde431ea96c1[\"Output\\nViolin - batch - log\"];\n 6 --> 15e501bc-8ddb-4519-89eb-dde431ea96c1;\n style 15e501bc-8ddb-4519-89eb-dde431ea96c1 stroke:#2c3143,stroke-width:4px;\n 7[\"Inspect AnnData\"];\n 0 -->|output| 7;\n 8[\"Plot\"];\n 0 -->|output| 8;\n eff22f46-baa6-4e00-ba82-d5e12ce26ff0[\"Output\\nScatter - mito x UMIs\"];\n 8 --> eff22f46-baa6-4e00-ba82-d5e12ce26ff0;\n style eff22f46-baa6-4e00-ba82-d5e12ce26ff0 stroke:#2c3143,stroke-width:4px;\n 9[\"Inspect AnnData\"];\n 0 -->|output| 9;\n 10[\"Plot\"];\n 0 -->|output| 10;\n 56677ca4-129c-476c-85ec-69d1bb3d800d[\"Output\\nViolin - sex - log\"];\n 10 --> 56677ca4-129c-476c-85ec-69d1bb3d800d;\n style 56677ca4-129c-476c-85ec-69d1bb3d800d stroke:#2c3143,stroke-width:4px;\n 11[\"Plot\"];\n 2 -->|output_h5ad| 11;\n acb61ea4-bcb9-45db-beef-e2bf1a176701[\"Output\\nViolin - Filterbygenes\"];\n 11 --> acb61ea4-bcb9-45db-beef-e2bf1a176701;\n style acb61ea4-bcb9-45db-beef-e2bf1a176701 stroke:#2c3143,stroke-width:4px;\n 12[\"Scanpy FilterCells\"];\n 2 -->|output_h5ad| 12;\n 51853662-4519-4229-a2ea-b22a53e7ef73[\"Output\\nCounts-filtered Object\"];\n 12 --> 51853662-4519-4229-a2ea-b22a53e7ef73;\n style 51853662-4519-4229-a2ea-b22a53e7ef73 stroke:#2c3143,stroke-width:4px;\n 13[\"Inspect AnnData\"];\n 2 -->|output_h5ad| 13;\n 362a7fe6-24bb-4398-ae48-870f4b4bb774[\"Output\\nGeneral - Filterbygenes\"];\n 13 --> 362a7fe6-24bb-4398-ae48-870f4b4bb774;\n style 362a7fe6-24bb-4398-ae48-870f4b4bb774 stroke:#2c3143,stroke-width:4px;\n 14[\"Inspect AnnData\"];\n 12 -->|output_h5ad| 14;\n edf24149-9341-4fe7-b10c-3fcf092faaa5[\"Output\\nGeneral - Filterbycounts\"];\n 14 --> edf24149-9341-4fe7-b10c-3fcf092faaa5;\n style edf24149-9341-4fe7-b10c-3fcf092faaa5 stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy FilterCells\"];\n 12 -->|output_h5ad| 15;\n a88ec405-265f-4a59-a75e-34e3b05b0096[\"Output\\nMito-filtered Object\"];\n 15 --> a88ec405-265f-4a59-a75e-34e3b05b0096;\n style a88ec405-265f-4a59-a75e-34e3b05b0096 stroke:#2c3143,stroke-width:4px;\n 16[\"Plot\"];\n 12 -->|output_h5ad| 16;\n a7c8b0d9-82d3-4438-a212-b5f7c56d36b8[\"Output\\nViolin - Filterbycounts\"];\n 16 --> a7c8b0d9-82d3-4438-a212-b5f7c56d36b8;\n style a7c8b0d9-82d3-4438-a212-b5f7c56d36b8 stroke:#2c3143,stroke-width:4px;\n 17[\"Inspect AnnData\"];\n 15 -->|output_h5ad| 17;\n 56882809-e19f-451a-8010-bc55dcee482f[\"Output\\nGeneral - Filterbymito\"];\n 17 --> 56882809-e19f-451a-8010-bc55dcee482f;\n style 56882809-e19f-451a-8010-bc55dcee482f stroke:#2c3143,stroke-width:4px;\n 18[\"Scanpy FilterGenes\"];\n 15 -->|output_h5ad| 18;\n 00846477-dec5-408a-83b2-105fff7ce05b[\"Output\\nFiltered Object\"];\n 18 --> 00846477-dec5-408a-83b2-105fff7ce05b;\n style 00846477-dec5-408a-83b2-105fff7ce05b stroke:#2c3143,stroke-width:4px;\n 19[\"Plot\"];\n 15 -->|output_h5ad| 19;\n 7582e113-2004-4255-a1f3-d3123373f342[\"Output\\nViolin - Filterbymito\"];\n 19 --> 7582e113-2004-4255-a1f3-d3123373f342;\n style 7582e113-2004-4255-a1f3-d3123373f342 stroke:#2c3143,stroke-width:4px;\n 20[\"Inspect AnnData\"];\n 18 -->|output_h5ad| 20;\n 2d870a40-c602-4a1c-afef-450489354d39[\"Output\\nGeneral - Filtered object\"];\n 20 --> 2d870a40-c602-4a1c-afef-450489354d39;\n style 2d870a40-c602-4a1c-afef-450489354d39 stroke:#2c3143,stroke-width:4px;\n 21[\"Scanpy NormaliseData\"];\n 18 -->|output_h5ad| 21;\n 22[\"Scanpy FindVariableGenes\"];\n 21 -->|output_h5ad| 22;\n a0eb92b1-0263-4179-b7af-4bd9bcc9c960[\"Output\\nUse_me_FVG\"];\n 22 --> a0eb92b1-0263-4179-b7af-4bd9bcc9c960;\n style a0eb92b1-0263-4179-b7af-4bd9bcc9c960 stroke:#2c3143,stroke-width:4px;\n 23[\"Scanpy ScaleData\"];\n 22 -->|output_h5ad| 23;\n 5776dbb9-0cac-40c0-9bae-9accae16a7a0[\"Output\\nUse_me_Scaled\"];\n 23 --> 5776dbb9-0cac-40c0-9bae-9accae16a7a0;\n style 5776dbb9-0cac-40c0-9bae-9accae16a7a0 stroke:#2c3143,stroke-width:4px;\n 24[\"Scanpy RunPCA\"];\n 23 -->|output_h5ad| 24;\n 25[\"Plot\"];\n 24 -->|output_h5ad| 25;\n f0b6f578-050f-4936-9ee7-9956b0760c6f[\"Output\\nPCA Variance\"];\n 25 --> f0b6f578-050f-4936-9ee7-9956b0760c6f;\n style f0b6f578-050f-4936-9ee7-9956b0760c6f stroke:#2c3143,stroke-width:4px;\n 26[\"Scanpy ComputeGraph\"];\n 24 -->|output_h5ad| 26;\n 27[\"Scanpy RunTSNE\"];\n 26 -->|output_h5ad| 27;\n 28[\"Scanpy RunUMAP\"];\n 27 -->|output_h5ad| 28;\n 29[\"Scanpy FindCluster\"];\n 28 -->|output_h5ad| 29;\n 30[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 30;\n 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3[\"Output\\nMarkers - cluster\"];\n 30 --> 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3;\n style 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3 stroke:#2c3143,stroke-width:4px;\n 98e98405-951e-4c6c-be01-3c925ae35449[\"Output\\nFinal object\"];\n 30 --> 98e98405-951e-4c6c-be01-3c925ae35449;\n style 98e98405-951e-4c6c-be01-3c925ae35449 stroke:#2c3143,stroke-width:4px;\n 31[\"Scanpy FindMarkers\"];\n 29 -->|output_h5ad| 31;\n 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4[\"Output\\nMarkers - genotype\"];\n 31 --> 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4;\n style 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4 stroke:#2c3143,stroke-width:4px;\n 32[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 32;\n 33[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 33;\n 34[\"Manipulate AnnData\"];\n 30 -->|output_h5ad| 34;\n 35[\"Scanpy PlotEmbed\"];\n 30 -->|output_h5ad| 35;\n 36[\"Inspect AnnData\"];\n 30 -->|output_h5ad| 36;\n 37[\"AnnData Operations\"];\n 34 -->|anndata| 37;\n 30 -->|output_h5ad| 37;\n 38[\"Join two Datasets\"];\n 30 -->|output_tsv| 38;\n 36 -->|var| 38;\n 39[\"Join two Datasets\"];\n 31 -->|output_tsv| 39;\n 36 -->|var| 39;\n 40[\"AnnData Operations\"];\n 37 -->|output_h5ad| 40;\n 10bd70f8-ffcb-442b-9647-e5b947b6d35e[\"Output\\nFinal cell annotated object\"];\n 40 --> 10bd70f8-ffcb-442b-9647-e5b947b6d35e;\n style 10bd70f8-ffcb-442b-9647-e5b947b6d35e stroke:#2c3143,stroke-width:4px;\n 41[\"Cut\"];\n 38 -->|out_file1| 41;\n 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e[\"Output\\nMarkers - cluster - named\"];\n 41 --> 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e;\n style 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e stroke:#2c3143,stroke-width:4px;\n 42[\"Cut\"];\n 39 -->|out_file1| 42;\n 3b471f3d-263d-4299-9b7d-8a8ae1aa556e[\"Output\\nMarkers - genotype - named\"];\n 42 --> 3b471f3d-263d-4299-9b7d-8a8ae1aa556e;\n style 3b471f3d-263d-4299-9b7d-8a8ae1aa556e stroke:#2c3143,stroke-width:4px;\n 43[\"Scanpy PlotEmbed\"];\n 40 -->|output_h5ad| 43;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
"outputs": [
{
@@ -723677,20 +671771,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n owner: iuc\n revisions: 55e35e9203cf\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n owner: iuc\n revisions: 9bd945a03d7b\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n owner: iuc\n revisions: aaa5da8e73a9\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n owner: iuc\n revisions: b409c2486353\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n owner: iuc\n revisions: c5d3684f7c4c\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n owner: iuc\n revisions: ab55fe8030b6\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n owner: iuc\n revisions: 6adf98e782f3\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n owner: iuc\n revisions: bf2017df9837\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
- "contributions": {
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- "mtekman",
- "beatrizserrano",
- "gallardoalba",
- "pavanvidem"
- ],
- "reviewing": [
- "mtekman",
- "nomadscientist",
- "hexylena",
- "beatrizserrano"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -723743,80 +671823,6 @@
"orcid": "0000-0002-5192-126X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "affiliations": [
- "uni-freiburg"
- ],
- "elixir_node": "de",
- "email": "mtekman89@gmail.com",
- "former_affiliations": [
- "elixir-europe"
- ],
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- "joined": "2018-11",
- "name": "Mehmet Tekman",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "bio": "Senior Lecturer at The Open University",
- "elixir_node": "uk",
- "email": "wendi.bacon@open.ac.uk",
- "fediverse": "https://mstdn.science/@wendibacon1",
- "fediverse_flavor": "mastodon",
- "id": "nomadscientist",
- "joined": "2020-03",
- "matrix": "nomadscientist:matrix.org",
- "name": "Wendi Bacon",
- "orcid": "0000-0002-8170-8806",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
- "twitter": "WendiBacon1",
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "id": "beatrizserrano",
- "joined": "2020-07",
- "linkedin": "beatriz-serrano",
- "matrix": "beatrizserrano:matrix.org",
- "name": "Beatriz Serrano-Solano",
- "orcid": "0000-0002-5862-6132",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
- "twitter": "BSerranoSolano",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
}
],
"dir": "topics/single-cell/tutorials/scrna-plant",
@@ -723855,7 +671861,7 @@
"Generate a DotPlot emulating the original paper using a different analysis tool",
"Determine robust clusters across scRNA-seq pipelines"
],
- "pageviews": 2618,
+ "pageviews": 2627,
"priority": 3,
"pub_date": "2021-04-08",
"questions": [
@@ -723892,14 +671898,14 @@
],
"short_id": "T00250",
"short_tools": [
- "scanpy_normalize",
- "anndata_manipulate",
- "scanpy_cluster_reduce_dimension",
- "scanpy_plot",
- "anndata_import",
"scanpy_remove_confounders",
+ "scanpy_normalize",
"scanpy_filter",
- "scanpy_inspect"
+ "anndata_import",
+ "scanpy_plot",
+ "anndata_manipulate",
+ "scanpy_inspect",
+ "scanpy_cluster_reduce_dimension"
],
"slides": false,
"slides_recordings": false,
@@ -723962,6 +671968,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -724017,10 +672027,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -724067,11 +672073,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -724116,6 +672117,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724168,10 +672173,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724204,12 +672205,12 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy1",
"0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
"0.6.22.post1+galaxy4",
- "0.6.22.post1+galaxy3"
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
+ "0.6.22.post1+galaxy1"
]
},
{
@@ -724224,10 +672225,6 @@
"state": "exact",
"version": "0.7.5+galaxy0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -724273,6 +672270,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724325,10 +672326,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724361,10 +672358,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.6.22.post1+galaxy2",
- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
},
@@ -724380,10 +672377,6 @@
"state": "exact",
"version": "0.7.5+galaxy0"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -724429,6 +672422,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724481,10 +672478,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724517,11 +672510,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2",
- "1.4.4+galaxy0"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy1"
]
},
{
@@ -724534,10 +672527,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -724583,6 +672572,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724635,10 +672628,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724671,11 +672660,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4+galaxy0",
- "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy1",
"1.4+galaxy0",
- "1.4.4.post1+galaxy2"
+ "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
+ "1.4.4.post1+galaxy0"
]
},
{
@@ -724688,10 +672677,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -724737,6 +672722,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724789,10 +672778,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724827,9 +672812,9 @@
"versions": [
"1.4.4+galaxy0",
"1.4.4.post1+galaxy0",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy2",
- "1.4+galaxy0"
+ "1.4.4.post1+galaxy2"
]
},
{
@@ -724842,10 +672827,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -724891,6 +672872,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -724943,10 +672928,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -724979,11 +672960,11 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4.4.post1+galaxy2",
+ "1.4+galaxy0",
"1.4.4.post1+galaxy0",
- "1.4.4+galaxy0",
+ "1.4.4.post1+galaxy2",
"1.4.4.post1+galaxy1",
- "1.4+galaxy0"
+ "1.4.4+galaxy0"
]
},
{
@@ -724996,10 +672977,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -725045,6 +673022,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -725097,10 +673078,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -725133,10 +673110,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.4+galaxy0",
"1.4.4.post1+galaxy1",
- "1.4.4.post1+galaxy0",
"1.4.4+galaxy0",
+ "1.4+galaxy0",
+ "1.4.4.post1+galaxy0",
"1.4.4.post1+galaxy2"
]
},
@@ -725152,10 +673129,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -725204,6 +673177,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -725256,10 +673233,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -725292,10 +673265,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
+ "1.4.4.post1",
"1.4.4.post1+galaxy2",
"1.4.4",
"1.4.4.post1+galaxy1",
- "1.4.4.post1",
"1.4"
]
},
@@ -725309,10 +673282,6 @@
"state": "exact",
"version": "1.7.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -725374,7 +673343,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 82,
- "visitors": 2079,
+ "visitors": 2087,
"workflows": [
{
"creators": [],
@@ -725623,7 +673592,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n style 0 fill:#ded,stroke:#393,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n style 5 fill:#ded,stroke:#393,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n style 6 fill:#ded,stroke:#393,stroke-width:4px;\n 7[\"Import Anndata and loom\"];\n 1 -->|output| 7;\n 8[\"Import Anndata and loom\"];\n 2 -->|output| 8;\n 9[\"Manipulate AnnData\"];\n 7 -->|anndata| 9;\n 8 -->|anndata| 9;\n 10[\"Rename Batches\"];\n 9 -->|anndata| 10;\n 680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n 10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n 11[\"QC metrics\"];\n 10 -->|anndata| 11;\n 12[\"Filter genes\"];\n 11 -->|anndata_out| 12;\n 3 -->|output| 12;\n 13[\"Plot Violin\"];\n 11 -->|anndata_out| 13;\n 14[\"Filter Cells\"];\n 12 -->|anndata_out| 14;\n 4 -->|output| 14;\n 15[\"Filter Max Features\"];\n 14 -->|anndata_out| 15;\n 5 -->|output| 15;\n 16[\"Filter Max Library Size\"];\n 15 -->|anndata| 16;\n 6 -->|output| 16;\n 17[\"Save RAW\"];\n 16 -->|anndata| 17;\n 18[\"Norm to 1e4\"];\n 17 -->|anndata| 18;\n 19[\"Log1p\"];\n 18 -->|anndata_out| 19;\n 20[\"Regress total counts\"];\n 19 -->|anndata_out| 20;\n 21[\"Scale\"];\n 20 -->|anndata_out| 21;\n 22[\"PCA\"];\n 21 -->|anndata_out| 22;\n 23[\"Neighborhod\"];\n 22 -->|anndata_out| 23;\n 24[\"UMAP\"];\n 23 -->|anndata_out| 24;\n 25[\"Leiden\"];\n 24 -->|anndata_out| 25;\n 0 -->|output| 25;\n 48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n 25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n 26[\"Plot PCA batch\"];\n 24 -->|anndata_out| 26;\n 27[\"Plot UMAP batch\"];\n 24 -->|anndata_out| 27;\n 28[\"Plot UMAP leiden, batch\"];\n 25 -->|anndata_out| 28;\n 29[\"Rename Clusters\"];\n 25 -->|anndata_out| 29;\n 30[\"Complex DotPlot\"];\n 25 -->|anndata_out| 30;\n 31[\"Complex DotPlot with new labels\"];\n 29 -->|anndata| 31;\n 32[\"Plot UMAP with new labels\"];\n 29 -->|anndata| 32;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "scRNA Plant Analysis",
"outputs": [
{
@@ -726355,7 +674324,7 @@
"Operate tools working on dataset collections",
"Compare plots resulting from different parameters values"
],
- "pageviews": 164,
+ "pageviews": 167,
"priority": 3,
"pub_date": "2023-07-19",
"questions": [
@@ -726376,12 +674345,12 @@
],
"short_id": "T00357",
"short_tools": [
- "scanpy_compute_graph",
+ "scanpy_plot_embed",
+ "scanpy_parameter_iterator",
+ "scanpy_find_cluster",
"scanpy_run_umap",
"scanpy_run_tsne",
- "scanpy_find_cluster",
- "scanpy_parameter_iterator",
- "scanpy_plot_embed"
+ "scanpy_compute_graph"
],
"slides": false,
"slides_recordings": false,
@@ -726428,6 +674397,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -726483,10 +674456,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -726533,11 +674502,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -726582,6 +674546,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -726634,10 +674602,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -726682,10 +674646,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -726733,6 +674693,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -726785,10 +674749,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -726833,10 +674793,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -726884,6 +674840,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -726936,10 +674896,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -726985,10 +674941,6 @@
"state": "exact",
"version": "0.0.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -727036,6 +674988,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -727088,10 +675044,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -727133,10 +675085,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -727181,6 +675129,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -727233,10 +675185,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -727281,10 +675229,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -727332,6 +675276,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -727384,10 +675332,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -727432,10 +675376,6 @@
"state": "exact",
"version": "1.8.1+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -727494,7 +675434,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 79,
- "visitors": 147,
+ "visitors": 150,
"workflows": [
{
"creators": [
@@ -727613,7 +675553,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nScanpy RunPCA: AnnData object\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"ParameterIterator n-neighbors\"];\n 2[\"\u2139\ufe0f Input Dataset\\nScanpy ComputeGraph on data X and data Y: Graph object AnnData\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"ParameterIterator perplexity\"];\n 4[\"\u2139\ufe0f Input Dataset\\nScanpy RunUMAP on data X: UMAP object AnnData\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"ParameterIterator resolution\"];\n 6[\"Scanpy ComputeGraph\"];\n 0 -->|output| 6;\n 1 -->|parameter_iteration| 6;\n 1e60c7cd-7e02-450f-a403-f3df1e548757[\"Output\\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)\"];\n 6 --> 1e60c7cd-7e02-450f-a403-f3df1e548757;\n style 1e60c7cd-7e02-450f-a403-f3df1e548757 stroke:#2c3143,stroke-width:4px;\n 7[\"Scanpy RunTSNE\"];\n 2 -->|output| 7;\n 3 -->|parameter_iteration| 7;\n 15143fea-5e2b-4b25-b5d1-0726da910f67[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)\"];\n 7 --> 15143fea-5e2b-4b25-b5d1-0726da910f67;\n style 15143fea-5e2b-4b25-b5d1-0726da910f67 stroke:#2c3143,stroke-width:4px;\n 8[\"Scanpy FindCluster\"];\n 4 -->|output| 8;\n 5 -->|parameter_iteration| 8;\n 6fdddfe7-c4da-4421-86a0-9819ce4c769c[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (resolution)\"];\n 8 --> 6fdddfe7-c4da-4421-86a0-9819ce4c769c;\n style 6fdddfe7-c4da-4421-86a0-9819ce4c769c stroke:#2c3143,stroke-width:4px;\n 9[\"Scanpy RunTSNE\"];\n 6 -->|output_h5ad| 9;\n 7c988247-b167-4733-859f-fcd582f91959[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)\"];\n 9 --> 7c988247-b167-4733-859f-fcd582f91959;\n style 7c988247-b167-4733-859f-fcd582f91959 stroke:#2c3143,stroke-width:4px;\n 10[\"Scanpy RunUMAP\"];\n 7 -->|output_h5ad| 10;\n 1f5abfa2-845c-4763-9f87-e4b167aa7bc8[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)\"];\n 10 --> 1f5abfa2-845c-4763-9f87-e4b167aa7bc8;\n style 1f5abfa2-845c-4763-9f87-e4b167aa7bc8 stroke:#2c3143,stroke-width:4px;\n 11[\"Scanpy PlotEmbed\"];\n 8 -->|output_h5ad| 11;\n 99185d1e-047f-47f2-9081-07506e1c17df[\"Output\\nresolution_pca_plots\"];\n 11 --> 99185d1e-047f-47f2-9081-07506e1c17df;\n style 99185d1e-047f-47f2-9081-07506e1c17df stroke:#2c3143,stroke-width:4px;\n 12[\"Scanpy PlotEmbed\"];\n 8 -->|output_h5ad| 12;\n 65d7b619-8659-4008-9e56-db21fda6ce8c[\"Output\\nresolution_umap_plots\"];\n 12 --> 65d7b619-8659-4008-9e56-db21fda6ce8c;\n style 65d7b619-8659-4008-9e56-db21fda6ce8c stroke:#2c3143,stroke-width:4px;\n 13[\"Scanpy PlotEmbed\"];\n 8 -->|output_h5ad| 13;\n bdcaf837-5fc4-4024-a87a-eabfa0110127[\"Output\\nresolution_tsne_plots\"];\n 13 --> bdcaf837-5fc4-4024-a87a-eabfa0110127;\n style bdcaf837-5fc4-4024-a87a-eabfa0110127 stroke:#2c3143,stroke-width:4px;\n 14[\"Scanpy RunUMAP\"];\n 9 -->|output_h5ad| 14;\n 8a0b3d69-e7df-4977-b8eb-ec478b914a26[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)\"];\n 14 --> 8a0b3d69-e7df-4977-b8eb-ec478b914a26;\n style 8a0b3d69-e7df-4977-b8eb-ec478b914a26 stroke:#2c3143,stroke-width:4px;\n 15[\"Scanpy FindCluster\"];\n 10 -->|output_h5ad| 15;\n c2e0d48f-9f0e-4452-8fb5-e78420578c65[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)\"];\n 15 --> c2e0d48f-9f0e-4452-8fb5-e78420578c65;\n style c2e0d48f-9f0e-4452-8fb5-e78420578c65 stroke:#2c3143,stroke-width:4px;\n 16[\"Scanpy FindCluster\"];\n 14 -->|output_h5ad| 16;\n c952b32e-99d5-4b94-a6d7-be59439c4dca[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)\"];\n 16 --> c952b32e-99d5-4b94-a6d7-be59439c4dca;\n style c952b32e-99d5-4b94-a6d7-be59439c4dca stroke:#2c3143,stroke-width:4px;\n 17[\"Scanpy PlotEmbed\"];\n 15 -->|output_h5ad| 17;\n 44c0ec07-b64e-428f-9254-5217e8041416[\"Output\\nperplexity_plots\"];\n 17 --> 44c0ec07-b64e-428f-9254-5217e8041416;\n style 44c0ec07-b64e-428f-9254-5217e8041416 stroke:#2c3143,stroke-width:4px;\n 18[\"Scanpy PlotEmbed\"];\n 16 -->|output_h5ad| 18;\n 0b30f573-8ebd-4582-9bcd-58ba5c778658[\"Output\\nn-neighbors_plots\"];\n 18 --> 0b30f573-8ebd-4582-9bcd-58ba5c778658;\n style 0b30f573-8ebd-4582-9bcd-58ba5c778658 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Scanpy Parameter Iterator workflow full (imported from URL)",
"outputs": [
{
@@ -728696,7 +676636,7 @@
"Convert raw gene expression data into the AnnData format.",
"Add metadata to the AnnData object to prepare it for analysis."
],
- "pageviews": 252,
+ "pageviews": 257,
"priority": 3,
"pub_date": "2023-12-13",
"questions": [
@@ -728716,15 +676656,15 @@
],
"short_id": "T00380",
"short_tools": [
+ "Cut1",
+ "tp_replace_in_column",
"unzip",
+ "anndata_ops",
+ "anndata_import",
"anndata_inspect",
+ "Paste1",
"anndata_manipulate",
- "anndata_import",
- "tp_replace_in_column",
- "anndata_ops",
- "scanpy_filter_cells",
- "Cut1",
- "Paste1"
+ "scanpy_filter_cells"
],
"slides": false,
"slides_recordings": false,
@@ -728766,6 +676706,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
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@@ -730649,7 +678546,7 @@
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],
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"questions": [
@@ -731798,6 +679555,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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},
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- "url": "http://galaxy.ul.edu.lb/"
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -731903,11 +679660,6 @@
"url": "https://usegalaxy.eu",
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},
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- "url": "https://usegalaxy.fr/",
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{
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"url": "https://usegalaxy.no/",
@@ -731952,6 +679704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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{
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"video_view": 0,
"visit_duration": 64,
- "visitors": 196,
+ "visitors": 198,
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- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "MuSiC-Deconvolution: Compare",
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{
@@ -732812,6 +680560,13 @@
"tool_panel_section_label": "Single-cell",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
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+ "owner": "ebi-gxa",
+ "revisions": "22bd5861706d",
+ "tool_panel_section_label": "Single-cell",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "scanpy_find_cluster",
"owner": "ebi-gxa",
@@ -732870,7 +680625,7 @@
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]
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+ "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scanpy_compute_graph\n owner: ebi-gxa\n revisions: 6417cccad133\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_compute_graph\n owner: ebi-gxa\n revisions: 22bd5861706d\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n owner: ebi-gxa\n revisions: ad6995afd2e6\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n owner: ebi-gxa\n revisions: 35f6611fb8c3\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_trajectory\n owner: ebi-gxa\n revisions: f489ccdd423c\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_diffmap\n owner: ebi-gxa\n revisions: e2ca1846080f\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_dpt\n owner: ebi-gxa\n revisions: 2e06dabb3f2f\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_fdg\n owner: ebi-gxa\n revisions: 7c6581b57ad4\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_paga\n owner: ebi-gxa\n revisions: 4e7d55438238\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n owner: iuc\n revisions: 3d748954434b\n tool_panel_section_label: Single-cell\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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@@ -733147,12 +680902,17 @@
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"edam_operation": [],
"edam_topic": [],
- "exact_supported_servers": [],
+ "exact_supported_servers": [
+ "UseGalaxy.eu"
+ ],
"feedback_mean_note": null,
"feedback_number": 0,
"hands_on": true,
"id": "single-cell/scrna-case_trajectories",
- "inexact_supported_servers": [],
+ "inexact_supported_servers": [
+ "UseGalaxy.org (Main)",
+ "UseGalaxy.org.au"
+ ],
"input_histories": [
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@@ -733169,12 +680929,12 @@
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"layout": "tutorial_hands_on",
"license": "CC-BY-4.0",
- "mod_date": "2024-10-28",
+ "mod_date": "2024-12-11",
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"Interpret these plots"
],
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"pub_date": "2023-12-08",
"questions": [
@@ -733193,22 +680953,39 @@
],
"short_id": "T00379",
"short_tools": [
- "scanpy_compute_graph",
- "scanpy_run_diffmap",
- "scanpy_run_dpt",
+ "scanpy_plot_embed",
"scanpy_plot_trajectory",
- "scanpy_run_fdg",
- "anndata_manipulate",
"scanpy_find_cluster",
+ "scanpy_run_dpt",
+ "scanpy_run_fdg",
+ "scanpy_run_diffmap",
"scanpy_run_paga",
- "scanpy_plot_embed"
+ "anndata_manipulate",
+ "scanpy_compute_graph"
],
"slides": false,
"slides_recordings": false,
"subtopic": "single-cell-CS",
"supported_servers": {
- "exact": [],
- "inexact": []
+ "exact": [
+ {
+ "name": "UseGalaxy.eu",
+ "url": "https://usegalaxy.eu",
+ "usegalaxy": true
+ }
+ ],
+ "inexact": [
+ {
+ "name": "UseGalaxy.org (Main)",
+ "url": "https://usegalaxy.org",
+ "usegalaxy": true
+ },
+ {
+ "name": "UseGalaxy.org.au",
+ "url": "https://usegalaxy.org.au",
+ "usegalaxy": true
+ }
+ ]
},
"supported_servers_matrix": {
"servers": [
@@ -733232,6 +681009,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -733287,10 +681068,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -733337,11 +681114,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -733364,7 +681136,7 @@
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+ "id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
"servers": [
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@@ -733386,6 +681158,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -733438,10 +681214,6 @@
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{
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},
{
"server": "https://usegalaxy.cz/",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
+ "1.4.3+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.eu",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
+ "state": "exact",
+ "version": "1.8.1+galaxy9"
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{
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- "state": "missing"
+ "state": "inexact",
+ "versions": [
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+ ]
},
{
"server": "https://usegalaxy.org",
- "state": "missing"
+ "state": "exact",
+ "version": "1.8.1+galaxy9"
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{
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- "state": "missing"
+ "state": "exact",
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],
- "version": "ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0"
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{
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"servers": [
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@@ -733528,6 +681305,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -733679,6 +681452,10 @@
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+ {
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{
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@@ -733794,10 +681563,10 @@
"server": "https://usegalaxy.org",
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"versions": [
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+ "1.8.1+galaxy9",
"1.7.2+galaxy0",
+ "1.8.1+2+galaxy0",
"1.9.3+galaxy0",
- "1.8.1+galaxy9",
"1.6.0+galaxy3"
]
},
@@ -733836,6 +681605,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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{
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@@ -733981,6 +681746,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -734134,6 +681895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -734284,6 +682041,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
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@@ -734434,6 +682187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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+ "state": "missing"
+ },
{
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -734636,10 +682389,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -734681,10 +682430,6 @@
"state": "exact",
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},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -734700,8 +682445,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.8.1+1+galaxy0"
+ "1.8.1+1+galaxy0",
+ "1.9.3+galaxy0"
]
},
{
@@ -734734,6 +682479,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -734786,10 +682535,6 @@
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -734822,10 +682567,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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- "0.6.22.post1+galaxy3",
- "0.6.19+galaxy0",
"0.6.22.post1+galaxy0",
+ "0.6.19+galaxy0",
+ "0.6.22.post1+galaxy3",
+ "0.6.22.post1+galaxy2",
"0.6.22.post1+galaxy1"
]
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@@ -734839,10 +682584,6 @@
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"version": "0.7.5+galaxy1"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -734876,8 +682617,8 @@
"time_estimation": "3H",
"title": "Inferring single cell trajectories with Scanpy",
"tools": [
- "https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0",
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+ "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0",
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
"toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9",
@@ -734902,12 +682643,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.json"
},
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+ "version": 10,
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"video_versions": 0,
"video_view": 0,
"visit_duration": 190,
- "visitors": 722,
+ "visitors": 734,
"workflows": [
{
"creators": [
@@ -734964,7 +682705,7 @@
],
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- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Inferring Trajectories with Scanpy Tutorial Workflow",
"outputs": [],
"parent_id": "single-cell/scrna-case_trajectories",
@@ -735341,7 +683082,7 @@
"You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
"You will create multiple ESet objects - both combined and separated out by disease phenotype for your single cell reference."
],
- "pageviews": 1096,
+ "pageviews": 1097,
"priority": 4,
"pub_date": "2023-01-20",
"questions": [
@@ -735359,23 +683100,23 @@
],
"short_id": "T00241",
"short_tools": [
+ "tp_sed_tool",
+ "Cut1",
+ "datamash_transpose",
+ "sort1",
"tp_easyjoin_tool",
+ "join1",
+ "tp_awk_tool",
"table_compute",
- "scanpy_read_10x",
"anndata_inspect",
- "tp_cut_tool",
- "tp_awk_tool",
- "music_construct_eset",
- "add_line_to_file",
"retrieve_scxa",
- "regex1",
- "sort1",
"annotatemyids",
- "join1",
- "tp_sed_tool",
- "Cut1",
+ "tp_cut_tool",
+ "add_line_to_file",
"music_manipulate_eset",
- "datamash_transpose"
+ "music_construct_eset",
+ "scanpy_read_10x",
+ "regex1"
],
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"slides_recordings": false,
@@ -735417,6 +683158,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -735472,10 +683217,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -735522,11 +683263,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -735571,6 +683307,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -735623,10 +683363,6 @@
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -735667,10 +683403,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -735713,6 +683445,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -735765,10 +683501,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -735809,10 +683541,6 @@
"server": "https://usegalaxy.eu",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
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"state": "local"
@@ -735855,6 +683583,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -735907,10 +683639,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -735951,10 +683679,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -735997,6 +683721,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736049,10 +683777,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -736096,10 +683820,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -736144,6 +683864,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736196,10 +683920,6 @@
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"state": "missing"
},
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- "state": "missing"
- },
{
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"state": "missing"
@@ -736242,10 +683962,6 @@
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -736290,6 +684006,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736342,10 +684062,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -736387,10 +684103,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -736435,6 +684147,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736489,10 +684205,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -736539,11 +684251,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -736589,6 +684296,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736643,10 +684354,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -736694,11 +684401,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -736744,6 +684446,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736798,10 +684504,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -736848,11 +684550,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -736898,6 +684595,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -736952,10 +684653,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -737002,11 +684699,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -737052,6 +684744,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737104,10 +684800,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -737152,13 +684844,6 @@
"state": "exact",
"version": "v0.0.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "v0.0.2+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -737210,6 +684895,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737262,10 +684951,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -737308,11 +684993,6 @@
"state": "exact",
"version": "v0.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "v0.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -737358,6 +685038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737410,10 +685094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
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@@ -737458,10 +685138,6 @@
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -737473,18 +685149,18 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.6.0+galaxy0",
+ "1.8.1+galaxy9",
"1.8.1+2+galaxy0",
- "1.8.1+galaxy9"
+ "1.9.3+galaxy0",
+ "1.6.0+galaxy0"
]
},
{
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
- "1.9.3+galaxy0",
- "1.8.1+1+galaxy0"
+ "1.8.1+1+galaxy0",
+ "1.9.3+galaxy0"
]
},
{
@@ -737517,6 +685193,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737575,10 +685255,6 @@
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{
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@@ -737630,11 +685306,6 @@
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},
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- "state": "exact",
- "version": "1.0.2"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -737682,6 +685353,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737734,10 +685409,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
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@@ -737771,10 +685442,10 @@
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"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -737788,10 +685459,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -737837,6 +685504,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -737890,10 +685561,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -737931,16 +685598,16 @@
"versions": [
"3.7.0",
"3.7.0+galaxy1",
- "3.5.0.1",
- "3.6.0"
+ "3.6.0",
+ "3.5.0.1"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.17.0+galaxy1",
- "3.16.0+galaxy1"
+ "3.16.0+galaxy1",
+ "3.17.0+galaxy1"
]
},
{
@@ -737948,19 +685615,14 @@
"state": "exact",
"version": "3.14.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.14.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"3.12.0",
- "3.12.0+galaxy1",
+ "3.7.0+galaxy2",
"3.14.0+galaxy0",
- "3.7.0+galaxy2"
+ "3.12.0+galaxy1"
]
},
{
@@ -738003,6 +685665,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -738059,10 +685725,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -738112,11 +685774,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -738162,6 +685819,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -738216,10 +685877,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -738266,11 +685923,6 @@
"state": "exact",
"version": "1.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -738341,7 +685993,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 140,
- "visitors": 621,
+ "visitors": 622,
"workflows": [
{
"creators": [
@@ -738403,7 +686055,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"EBI SCXA Data Retrieval\"];\n 1[\"\u2139\ufe0f Input Dataset\\nSingle cell metadata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Scanpy Read10x\"];\n 0 -->|barcode_tsv| 2;\n 0 -->|genes_tsv| 2;\n 0 -->|matrix_mtx| 2;\n 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d[\"Output\\nScanpy Read10x on input dataset(s): anndata\"];\n 2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;\n style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;\n 3[\"Inspect AnnData\"];\n 2 -->|output_h5| 3;\n 4[\"Transpose\"];\n 3 -->|X| 4;\n 5[\"annotateMyIDs\"];\n 4 -->|out_file| 5;\n c39c7d69-550e-4b54-a412-317b599c5e55[\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"];\n 5 --> c39c7d69-550e-4b54-a412-317b599c5e55;\n style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;\n 6[\"\ud83d\udee0\ufe0f Subworkflow\\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes\"];\n style 6 fill:#edd,stroke:#900,stroke-width:4px;\n 5 -->|out_tab| 6;\n 4 -->|out_file| 6;\n 7[\"Construct Expression Set Object\"];\n 6 -->|Gene Symbol Count Matrix| 7;\n 1 -->|output| 7;\n e8c91df0-4e6c-4eb2-9807-c2679b494958[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n 7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;\n style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;\n 2912d09b-b178-4035-b7c8-7038392e2bf2[\"Output\\nConstruct Expression Set Object on input dataset(s): General Info\"];\n 7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;\n style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;\n 8[\"Manipulate Expression Set Object\"];\n 7 -->|out_rds| 8;\n 08de92d8-32fe-4b47-9038-298cdd13fac5[\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"];\n 8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;\n style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;\n 9[\"Manipulate Expression Set Object\"];\n 7 -->|out_rds| 9;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
"outputs": [
{
@@ -739483,7 +687135,7 @@
"inputs": [],
"license": null,
"mermaid": "flowchart TD\n 0[\"EBI SCXA Data Retrieval\"];\n 1[\"Cut\"];\n 0 -->|design_tsv| 1;\n 2[\"Add line to file\"];\n 0 -->|barcode_tsv| 2;\n 3[\"Reformatting metadata columns\"];\n 1 -->|out_file1| 3;\n 4[\"Join two Datasets\"];\n 2 -->|outfile| 4;\n 3 -->|out_file1| 4;\n 5[\"Advanced Cut\"];\n 4 -->|out_file1| 5;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "MuSiC-Deconvolution: Data generation | sc | metadata",
"outputs": [
{
@@ -739851,21 +687503,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/tutorial.json",
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- "nomadscientist",
- "kkamieniecka"
- ],
- "reviewing": [
- "teresa-m",
- "shiltemann",
- "pavanvidem",
- "MarisaJL",
- "hexhowells",
- "bgruening"
- ]
- },
"contributors": [
{
"email": "hexhowells@gmail.com",
@@ -739906,112 +687543,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
"twitter": "katemurat",
"url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
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- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "pavanvidem",
- "joined": "2017-09",
- "name": "Pavankumar Videm",
- "orcid": "0000-0002-5192-126X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
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- "id": "MarisaJL",
- "joined": "2022-10",
- "name": "Marisa Loach",
- "orcid": "0000-0001-6979-6930",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
- "twitter": "Marisa_Loach",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
- },
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- "id": "hexhowells",
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- "name": "Morgan Howells",
- "orcid": "0009-0008-9422-6380",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
- },
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/single-cell/tutorials/scrna-data-formats",
@@ -740048,7 +687579,7 @@
"Learn the common data formats used for storing single-cell data",
"Become familiar with some popular sources for public single-cell data"
],
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+ "pageviews": 546905,
"priority": 4,
"pub_date": "2024-07-26",
"questions": [
@@ -740157,8 +687688,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 164,
- "visitors": 206866
+ "visit_duration": 163,
+ "visitors": 216483
},
{
"admin_install": {
@@ -740430,7 +687961,7 @@
"Compare the outputs from Scanpy, Monocle in Galaxy and Monocle in R",
"Describe differential expression analysis methods"
],
- "pageviews": 5065,
+ "pageviews": 5103,
"priority": 4,
"pub_date": "2023-04-12",
"questions": [
@@ -740523,7 +688054,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 52,
- "visitors": 4398,
+ "visitors": 4430,
"zenodo_link": "https://zenodo.org/record/7455590"
},
{
@@ -740916,7 +688447,7 @@
"Compare the outputs from Scanpy and Monocle",
"Interpet trajectory analysis results"
],
- "pageviews": 3799,
+ "pageviews": 3817,
"priority": 5,
"pub_date": "2022-09-30",
"questions": [
@@ -740957,22 +688488,22 @@
],
"short_id": "T00249",
"short_tools": [
- "monocle3_partition",
+ "monocle3_topmarkers",
+ "Filter1",
+ "Cut1",
+ "datamash_transpose",
+ "monocle3_learnGraph",
+ "join1",
"monocle3_reduceDim",
- "anndata_inspect",
"regexColumn1",
- "tp_cut_tool",
"monocle3_plotCells",
"monocle3_create",
- "monocle3_learnGraph",
- "Filter1",
- "join1",
"monocle3_orderCells",
- "Cut1",
- "monocle3_topmarkers",
- "monocle3_preprocess",
+ "anndata_inspect",
+ "tp_cut_tool",
"monocle3_diffExp",
- "datamash_transpose"
+ "monocle3_preprocess",
+ "monocle3_partition"
],
"slides": false,
"slides_recordings": false,
@@ -741014,6 +688545,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -741069,10 +688604,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -741119,11 +688650,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -741168,6 +688694,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -741220,10 +688750,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -741264,10 +688790,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -741310,6 +688832,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -741362,10 +688888,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -741406,10 +688928,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -741452,6 +688970,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -741504,10 +689026,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -741548,10 +689066,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -741594,6 +689108,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -741648,10 +689166,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -741699,11 +689213,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
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- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -741749,6 +689258,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -741801,10 +689314,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -741846,10 +689355,6 @@
"state": "exact",
"version": "0.1.4+galaxy2"
},
- {
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- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -741893,6 +689398,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -741945,10 +689454,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -741990,10 +689495,6 @@
"state": "exact",
"version": "0.1.4+galaxy1"
},
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742037,6 +689538,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742089,10 +689594,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742134,10 +689635,6 @@
"state": "exact",
"version": "0.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742181,6 +689678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742233,10 +689734,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742278,10 +689775,6 @@
"state": "exact",
"version": "0.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742325,6 +689818,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742377,10 +689874,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742422,10 +689915,6 @@
"state": "exact",
"version": "0.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742469,6 +689958,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742521,10 +690014,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742566,10 +690055,6 @@
"state": "exact",
"version": "0.1.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742613,6 +690098,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742665,10 +690154,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742710,10 +690195,6 @@
"state": "exact",
"version": "0.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742757,6 +690238,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742809,10 +690294,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742854,10 +690335,6 @@
"state": "exact",
"version": "0.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -742901,6 +690378,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -742953,10 +690434,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -742998,10 +690475,6 @@
"state": "exact",
"version": "0.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -743045,6 +690518,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -743103,10 +690580,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -743158,11 +690631,6 @@
"state": "exact",
"version": "1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -743210,6 +690678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -743262,10 +690734,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -743299,10 +690767,10 @@
"state": "inexact",
"versions": [
"0.6.22.post1+galaxy3",
- "0.6.22.post1+galaxy0",
- "0.6.22.post1+galaxy2",
"0.7.4+galaxy1",
"0.6.22.post1+galaxy1",
+ "0.6.22.post1+galaxy0",
+ "0.6.22.post1+galaxy2",
"0.6.19+galaxy0"
]
},
@@ -743316,10 +690784,6 @@
"state": "exact",
"version": "0.7.5+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -743365,6 +690829,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -743421,10 +690889,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -743474,11 +690938,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -743548,8 +691007,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 92,
- "visitors": 3038,
+ "visit_duration": 91,
+ "visitors": 3055,
"workflows": [
{
"creators": [],
@@ -743626,7 +691085,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Extract cell annotations\"];\n 0 -->|output| 2;\n 9d66a217-4269-4fb4-9a4e-520eedbb0c9d[\"Output\\nExtracted cell annotations (obs)\"];\n 2 --> 9d66a217-4269-4fb4-9a4e-520eedbb0c9d;\n style 9d66a217-4269-4fb4-9a4e-520eedbb0c9d stroke:#2c3143,stroke-width:4px;\n 3[\"Extract gene annotations\"];\n 0 -->|output| 3;\n 03537e97-d668-4ce2-ba6b-2952a18a2752[\"Output\\nExtracted gene annotations (var)\"];\n 3 --> 03537e97-d668-4ce2-ba6b-2952a18a2752;\n style 03537e97-d668-4ce2-ba6b-2952a18a2752 stroke:#2c3143,stroke-width:4px;\n 4[\"Extract clean expression matrix\"];\n 1 -->|output| 4;\n 963462c8-4ae0-486c-8173-d98339127850[\"Output\\nUnprocessed expression matrix\"];\n 4 --> 963462c8-4ae0-486c-8173-d98339127850;\n style 963462c8-4ae0-486c-8173-d98339127850 stroke:#2c3143,stroke-width:4px;\n 5[\"Filter out unwanted cell types\"];\n 2 -->|obs| 5;\n 5dcb7029-8d03-445d-bb3e-a3119e502be4[\"Output\\nCells without macrophages\"];\n 5 --> 5dcb7029-8d03-445d-bb3e-a3119e502be4;\n style 5dcb7029-8d03-445d-bb3e-a3119e502be4 stroke:#2c3143,stroke-width:4px;\n 6[\"gene_short_name annotation\"];\n 3 -->|var| 6;\n 15fd415b-2d73-4a1d-92ad-200bb2e73853[\"Output\\nGenes table with gene_short_name colname\"];\n 6 --> 15fd415b-2d73-4a1d-92ad-200bb2e73853;\n style 15fd415b-2d73-4a1d-92ad-200bb2e73853 stroke:#2c3143,stroke-width:4px;\n 7[\"Cut cells IDs\"];\n 5 -->|out_file1| 7;\n f9bde249-43b9-4424-8285-e437549223e2[\"Output\\nFiltered cells IDs \"];\n 7 --> f9bde249-43b9-4424-8285-e437549223e2;\n style f9bde249-43b9-4424-8285-e437549223e2 stroke:#2c3143,stroke-width:4px;\n 8[\"Cut genes IDs\"];\n 6 -->|out_file1| 8;\n b22efa1d-db99-435f-9357-74150ac9a437[\"Output\\nGenes IDs\"];\n 8 --> b22efa1d-db99-435f-9357-74150ac9a437;\n style b22efa1d-db99-435f-9357-74150ac9a437 stroke:#2c3143,stroke-width:4px;\n 9[\"Filter matrix by cells\"];\n 7 -->|out_file1| 9;\n 4 -->|X| 9;\n b45f18b6-e385-41a1-a8f0-f94e6616e2b3[\"Output\\nPre-filtered matrix (by cells)\"];\n 9 --> b45f18b6-e385-41a1-a8f0-f94e6616e2b3;\n style b45f18b6-e385-41a1-a8f0-f94e6616e2b3 stroke:#2c3143,stroke-width:4px;\n 10[\"Remove duplicate column cells IDs\"];\n 9 -->|out_file1| 10;\n f4d6a581-9b42-41dc-9a4a-278fe5d6591c[\"Output\\nFiltered matrix (by cells) \"];\n 10 --> f4d6a581-9b42-41dc-9a4a-278fe5d6591c;\n style f4d6a581-9b42-41dc-9a4a-278fe5d6591c stroke:#2c3143,stroke-width:4px;\n 11[\"Transpose matrix\"];\n 10 -->|output| 11;\n e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5[\"Output\\nfiltered matrix (by cells) transposed\"];\n 11 --> e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5;\n style e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5 stroke:#2c3143,stroke-width:4px;\n 12[\"Filter matrix by genes\"];\n 8 -->|out_file1| 12;\n 11 -->|out_file| 12;\n c0481255-0187-407c-9f29-f4c0069d9285[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n 12 --> c0481255-0187-407c-9f29-f4c0069d9285;\n style c0481255-0187-407c-9f29-f4c0069d9285 stroke:#2c3143,stroke-width:4px;\n 13[\"Remove duplicate column genes IDs\"];\n 12 -->|out_file1| 13;\n 4dcd8e60-1298-4886-be8f-af1eac9f20f7[\"Output\\nFiltered matrix (by cells & genes)\"];\n 13 --> 4dcd8e60-1298-4886-be8f-af1eac9f20f7;\n style 4dcd8e60-1298-4886-be8f-af1eac9f20f7 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "AnnData object to Monocle input files",
"outputs": [
{
@@ -744377,7 +691836,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nExpression matrix input\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nCell annotations input\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nGene annotations input\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Monocle3 create\"];\n 1 -->|output| 3;\n 0 -->|output| 3;\n 2 -->|output| 3;\n 30db218d-f9e5-426d-ac9b-7823743ab5fb[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n 3 --> 30db218d-f9e5-426d-ac9b-7823743ab5fb;\n style 30db218d-f9e5-426d-ac9b-7823743ab5fb stroke:#2c3143,stroke-width:4px;\n 4[\"Monocle3 preprocess\"];\n 3 -->|output_rds| 4;\n 38996ee0-0c00-4a01-ad18-f2e505eaf780[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n 4 --> 38996ee0-0c00-4a01-ad18-f2e505eaf780;\n style 38996ee0-0c00-4a01-ad18-f2e505eaf780 stroke:#2c3143,stroke-width:4px;\n 5[\"Monocle3 reduceDim\"];\n 4 -->|output_rds| 5;\n 21edf68f-72df-457d-aad7-c5fc5afa2b6b[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n 5 --> 21edf68f-72df-457d-aad7-c5fc5afa2b6b;\n style 21edf68f-72df-457d-aad7-c5fc5afa2b6b stroke:#2c3143,stroke-width:4px;\n 6[\"Monocle3 partition\"];\n 5 -->|output_rds| 6;\n fdb0e520-27c4-43a0-8f27-a25832a0816d[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n 6 --> fdb0e520-27c4-43a0-8f27-a25832a0816d;\n style fdb0e520-27c4-43a0-8f27-a25832a0816d stroke:#2c3143,stroke-width:4px;\n 7[\"Plot cell type\"];\n 5 -->|output_rds| 7;\n 5e309658-e20f-4da1-8841-818f16fa8f01[\"Output\\nCell type plot\"];\n 7 --> 5e309658-e20f-4da1-8841-818f16fa8f01;\n style 5e309658-e20f-4da1-8841-818f16fa8f01 stroke:#2c3143,stroke-width:4px;\n 8[\"Plot genotype\"];\n 5 -->|output_rds| 8;\n aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4[\"Output\\nGenotype plot\"];\n 8 --> aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4;\n style aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4 stroke:#2c3143,stroke-width:4px;\n 9[\"Plot batch\"];\n 5 -->|output_rds| 9;\n c8eec2e4-1a64-47bb-812b-4002968c57c8[\"Output\\nBatch plot\"];\n 9 --> c8eec2e4-1a64-47bb-812b-4002968c57c8;\n style c8eec2e4-1a64-47bb-812b-4002968c57c8 stroke:#2c3143,stroke-width:4px;\n 10[\"Plot sex\"];\n 5 -->|output_rds| 10;\n c75954dd-34d5-4a20-bcf3-e5cd92d74885[\"Output\\nSex plot\"];\n 10 --> c75954dd-34d5-4a20-bcf3-e5cd92d74885;\n style c75954dd-34d5-4a20-bcf3-e5cd92d74885 stroke:#2c3143,stroke-width:4px;\n 11[\"Monocle3 top markers\"];\n 6 -->|output_rds| 11;\n 12[\"Plot genes\"];\n 6 -->|output_rds| 12;\n f91c22a3-8c6d-432a-92c5-cb010115fa86[\"Output\\nGene expression plot\"];\n 12 --> f91c22a3-8c6d-432a-92c5-cb010115fa86;\n style f91c22a3-8c6d-432a-92c5-cb010115fa86 stroke:#2c3143,stroke-width:4px;\n 13[\"Plot partition\"];\n 6 -->|output_rds| 13;\n f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d[\"Output\\nPartition plot\"];\n 13 --> f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d;\n style f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d stroke:#2c3143,stroke-width:4px;\n 14[\"Plot cluster\"];\n 6 -->|output_rds| 14;\n a2c1a628-d79d-4e37-ad33-de92033021a8[\"Output\\nCluster plot\"];\n 14 --> a2c1a628-d79d-4e37-ad33-de92033021a8;\n style a2c1a628-d79d-4e37-ad33-de92033021a8 stroke:#2c3143,stroke-width:4px;\n 15[\"Monocle3 learnGraph\"];\n 6 -->|output_rds| 15;\n ed2003aa-4680-409f-8d79-e79b878a786c[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n 15 --> ed2003aa-4680-409f-8d79-e79b878a786c;\n style ed2003aa-4680-409f-8d79-e79b878a786c stroke:#2c3143,stroke-width:4px;\n 16[\"Plot learned trajectory\"];\n 15 -->|output_rds| 16;\n 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d[\"Output\\nCell types & learned trajectory path plot\"];\n 16 --> 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d;\n style 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d stroke:#2c3143,stroke-width:4px;\n 17[\"Monocle3 orderCells\"];\n 15 -->|output_rds| 17;\n 96d10412-3d7f-4970-b541-6f4367fa3f37[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n 17 --> 96d10412-3d7f-4970-b541-6f4367fa3f37;\n style 96d10412-3d7f-4970-b541-6f4367fa3f37 stroke:#2c3143,stroke-width:4px;\n 18[\"Monocle3 diffExp\"];\n 17 -->|output_rds| 18;\n db1dc457-2d6e-47cc-b7ce-d0a4d23e9498[\"Output\\nDifferential expression of genes - table\"];\n 18 --> db1dc457-2d6e-47cc-b7ce-d0a4d23e9498;\n style db1dc457-2d6e-47cc-b7ce-d0a4d23e9498 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot pseudotime\"];\n 17 -->|output_rds| 19;\n d1b3efd2-0a81-4dad-8652-589c2678fbaa[\"Output\\nPseudotime plot\"];\n 19 --> d1b3efd2-0a81-4dad-8652-589c2678fbaa;\n style d1b3efd2-0a81-4dad-8652-589c2678fbaa stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Monocle3 workflow",
"outputs": [
{
@@ -745361,7 +692820,7 @@
],
"license": "CC-BY-4.0",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Extract cell annotations\"];\n 0 -->|output| 2;\n 0646798d-3a5d-420a-a7cf-cde6cec722d5[\"Output\\nExtracted cell annotations (obs)\"];\n 2 --> 0646798d-3a5d-420a-a7cf-cde6cec722d5;\n style 0646798d-3a5d-420a-a7cf-cde6cec722d5 stroke:#2c3143,stroke-width:4px;\n 3[\"Extract gene annotations\"];\n 0 -->|output| 3;\n 84162745-68b0-41a5-b06e-a285440ba095[\"Output\\nExtracted gene annotations (var)\"];\n 3 --> 84162745-68b0-41a5-b06e-a285440ba095;\n style 84162745-68b0-41a5-b06e-a285440ba095 stroke:#2c3143,stroke-width:4px;\n 4[\"Extract clean expression matrix\"];\n 1 -->|output| 4;\n 3f03af0c-ac41-4450-b5ba-639a79ea543b[\"Output\\nUnprocessed expression matrix\"];\n 4 --> 3f03af0c-ac41-4450-b5ba-639a79ea543b;\n style 3f03af0c-ac41-4450-b5ba-639a79ea543b stroke:#2c3143,stroke-width:4px;\n 5[\"Filter out macrophages\"];\n 2 -->|obs| 5;\n fb81e9a1-0603-419a-83f5-0c9f94939b16[\"Output\\nCells without macrophages\"];\n 5 --> fb81e9a1-0603-419a-83f5-0c9f94939b16;\n style fb81e9a1-0603-419a-83f5-0c9f94939b16 stroke:#2c3143,stroke-width:4px;\n 6[\"gene_short_name annotation\"];\n 3 -->|var| 6;\n 94a60e6c-cdf7-48e5-8b55-d221cef22688[\"Output\\nGenes table with gene_short_name colname\"];\n 6 --> 94a60e6c-cdf7-48e5-8b55-d221cef22688;\n style 94a60e6c-cdf7-48e5-8b55-d221cef22688 stroke:#2c3143,stroke-width:4px;\n 7[\"Cut cells IDs\"];\n 5 -->|out_file1| 7;\n 34146c30-2666-481f-8d49-a849d5d3aa91[\"Output\\nFiltered cells IDs \"];\n 7 --> 34146c30-2666-481f-8d49-a849d5d3aa91;\n style 34146c30-2666-481f-8d49-a849d5d3aa91 stroke:#2c3143,stroke-width:4px;\n 8[\"Cut genes IDs\"];\n 6 -->|out_file1| 8;\n 8f38fb93-cb30-4fbc-90c5-7f6bd023feea[\"Output\\nGenes IDs\"];\n 8 --> 8f38fb93-cb30-4fbc-90c5-7f6bd023feea;\n style 8f38fb93-cb30-4fbc-90c5-7f6bd023feea stroke:#2c3143,stroke-width:4px;\n 9[\"Filter matrix by cells\"];\n 7 -->|out_file1| 9;\n 4 -->|X| 9;\n f654c045-5fea-43f9-96d6-492c810593d2[\"Output\\nPre-filtered matrix (by cells)\"];\n 9 --> f654c045-5fea-43f9-96d6-492c810593d2;\n style f654c045-5fea-43f9-96d6-492c810593d2 stroke:#2c3143,stroke-width:4px;\n 10[\"Remove duplicate column cells IDs\"];\n 9 -->|out_file1| 10;\n f633c125-a4d0-4fa7-ab87-022349f4ac70[\"Output\\nFiltered matrix (by cells) \"];\n 10 --> f633c125-a4d0-4fa7-ab87-022349f4ac70;\n style f633c125-a4d0-4fa7-ab87-022349f4ac70 stroke:#2c3143,stroke-width:4px;\n 11[\"Transpose matrix\"];\n 10 -->|output| 11;\n 3202091e-1afc-4f50-8922-1f9e50c490fc[\"Output\\nfiltered matrix (by cells) transposed\"];\n 11 --> 3202091e-1afc-4f50-8922-1f9e50c490fc;\n style 3202091e-1afc-4f50-8922-1f9e50c490fc stroke:#2c3143,stroke-width:4px;\n 12[\"Filter matrix by genes\"];\n 8 -->|out_file1| 12;\n 11 -->|out_file| 12;\n 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n 12 --> 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88;\n style 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88 stroke:#2c3143,stroke-width:4px;\n 13[\"Remove duplicate column genes IDs\"];\n 12 -->|out_file1| 13;\n 25839326-0b5d-4e74-91ec-24e22c08f7c5[\"Output\\nFiltered matrix (by cells & genes)\"];\n 13 --> 25839326-0b5d-4e74-91ec-24e22c08f7c5;\n style 25839326-0b5d-4e74-91ec-24e22c08f7c5 stroke:#2c3143,stroke-width:4px;\n 14[\"Monocle3 create\"];\n 5 -->|out_file1| 14;\n 13 -->|output| 14;\n 6 -->|out_file1| 14;\n f8c5589c-a70d-416e-a9de-ebc987f61fc3[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n 14 --> f8c5589c-a70d-416e-a9de-ebc987f61fc3;\n style f8c5589c-a70d-416e-a9de-ebc987f61fc3 stroke:#2c3143,stroke-width:4px;\n 15[\"Monocle3 preprocess\"];\n 14 -->|output_rds| 15;\n c134942f-60e7-4cd0-8c32-da4a303b879d[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n 15 --> c134942f-60e7-4cd0-8c32-da4a303b879d;\n style c134942f-60e7-4cd0-8c32-da4a303b879d stroke:#2c3143,stroke-width:4px;\n 16[\"Monocle3 reduceDim\"];\n 15 -->|output_rds| 16;\n 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n 16 --> 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1;\n style 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1 stroke:#2c3143,stroke-width:4px;\n 17[\"Monocle3 partition\"];\n 16 -->|output_rds| 17;\n 93371c10-6583-47fc-830f-9a90dc980766[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n 17 --> 93371c10-6583-47fc-830f-9a90dc980766;\n style 93371c10-6583-47fc-830f-9a90dc980766 stroke:#2c3143,stroke-width:4px;\n 18[\"Plot cell type\"];\n 16 -->|output_rds| 18;\n f096d060-82e8-4847-9e8f-b22c9288f565[\"Output\\nCell type plot\"];\n 18 --> f096d060-82e8-4847-9e8f-b22c9288f565;\n style f096d060-82e8-4847-9e8f-b22c9288f565 stroke:#2c3143,stroke-width:4px;\n 19[\"Plot genotype\"];\n 16 -->|output_rds| 19;\n aab28bb1-e2e7-4b7d-9b2b-1cab64bea287[\"Output\\nGenotype plot\"];\n 19 --> aab28bb1-e2e7-4b7d-9b2b-1cab64bea287;\n style aab28bb1-e2e7-4b7d-9b2b-1cab64bea287 stroke:#2c3143,stroke-width:4px;\n 20[\"Plot batch\"];\n 16 -->|output_rds| 20;\n 9b362eee-9238-47c5-a4c2-85f3995430f4[\"Output\\nBatch plot\"];\n 20 --> 9b362eee-9238-47c5-a4c2-85f3995430f4;\n style 9b362eee-9238-47c5-a4c2-85f3995430f4 stroke:#2c3143,stroke-width:4px;\n 21[\"Plot sex\"];\n 16 -->|output_rds| 21;\n c2a1e104-ef2d-4b66-ac2b-bf0251714434[\"Output\\nSex plot\"];\n 21 --> c2a1e104-ef2d-4b66-ac2b-bf0251714434;\n style c2a1e104-ef2d-4b66-ac2b-bf0251714434 stroke:#2c3143,stroke-width:4px;\n 22[\"Monocle3 top markers\"];\n 17 -->|output_rds| 22;\n 23[\"Plot genes\"];\n 17 -->|output_rds| 23;\n e8867379-82c6-4c32-a2d3-0b24670269ae[\"Output\\nGene expression plot\"];\n 23 --> e8867379-82c6-4c32-a2d3-0b24670269ae;\n style e8867379-82c6-4c32-a2d3-0b24670269ae stroke:#2c3143,stroke-width:4px;\n 24[\"Plot partition\"];\n 17 -->|output_rds| 24;\n 3f7b0a7c-85d6-430b-8385-fa9a76385c0e[\"Output\\nPartition plot\"];\n 24 --> 3f7b0a7c-85d6-430b-8385-fa9a76385c0e;\n style 3f7b0a7c-85d6-430b-8385-fa9a76385c0e stroke:#2c3143,stroke-width:4px;\n 25[\"Plot cluster\"];\n 17 -->|output_rds| 25;\n 40b65826-f73e-4054-a56d-b241985d6996[\"Output\\nCluster plot\"];\n 25 --> 40b65826-f73e-4054-a56d-b241985d6996;\n style 40b65826-f73e-4054-a56d-b241985d6996 stroke:#2c3143,stroke-width:4px;\n 26[\"Monocle3 learnGraph\"];\n 17 -->|output_rds| 26;\n 294b1a49-cec6-49d0-bcd4-3a954da67bec[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n 26 --> 294b1a49-cec6-49d0-bcd4-3a954da67bec;\n style 294b1a49-cec6-49d0-bcd4-3a954da67bec stroke:#2c3143,stroke-width:4px;\n 27[\"Plot learned trajectory\"];\n 26 -->|output_rds| 27;\n c85ddefe-8eaf-4d21-93ed-ca0859286bf0[\"Output\\nCell types & learned trajectory path plot\"];\n 27 --> c85ddefe-8eaf-4d21-93ed-ca0859286bf0;\n style c85ddefe-8eaf-4d21-93ed-ca0859286bf0 stroke:#2c3143,stroke-width:4px;\n 28[\"Monocle3 orderCells\"];\n 26 -->|output_rds| 28;\n 5aea5752-b767-4fc8-8741-1f4d1c659a41[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n 28 --> 5aea5752-b767-4fc8-8741-1f4d1c659a41;\n style 5aea5752-b767-4fc8-8741-1f4d1c659a41 stroke:#2c3143,stroke-width:4px;\n 29[\"Monocle3 diffExp\"];\n 28 -->|output_rds| 29;\n 3c298624-9f06-4e52-b2a8-fb834b87c296[\"Output\\nDifferential expression of genes - table\"];\n 29 --> 3c298624-9f06-4e52-b2a8-fb834b87c296;\n style 3c298624-9f06-4e52-b2a8-fb834b87c296 stroke:#2c3143,stroke-width:4px;\n 30[\"Plot pseudotime\"];\n 28 -->|output_rds| 30;\n 813d15bb-0771-4aed-9226-4874c1ddba59[\"Output\\nPseudotime plot\"];\n 30 --> 813d15bb-0771-4aed-9226-4874c1ddba59;\n style 813d15bb-0771-4aed-9226-4874c1ddba59 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Trajectory analysis using Monocle3 - full tutorial workflow",
"outputs": [
{
@@ -747226,7 +694685,7 @@
"You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
"You will create multiple ESet objects - both combined and separated out by disease phenotype for your bulk dataset."
],
- "pageviews": 909,
+ "pageviews": 912,
"priority": 5,
"pub_date": "2023-01-20",
"questions": [
@@ -747245,17 +694704,17 @@
],
"short_id": "T00242",
"short_tools": [
- "tp_easyjoin_tool",
+ "tp_sed_tool",
"column_remove_by_header",
+ "sort1",
+ "tp_easyjoin_tool",
"table_compute",
- "tp_cut_tool",
"tp_awk_tool",
- "music_construct_eset",
- "regex1",
- "sort1",
"annotatemyids",
- "tp_sed_tool",
- "music_manipulate_eset"
+ "tp_cut_tool",
+ "music_manipulate_eset",
+ "regex1",
+ "music_construct_eset"
],
"slides": false,
"slides_recordings": false,
@@ -747298,6 +694757,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -747353,10 +694816,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -747403,11 +694862,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -747452,6 +694906,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -747504,10 +694962,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -747548,10 +695002,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -747594,6 +695044,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -747646,10 +695100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -747692,10 +695142,6 @@
"state": "exact",
"version": "0.1.1+galaxy4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -747740,6 +695186,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -747792,10 +695242,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -747837,10 +695283,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -747885,6 +695327,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -747939,10 +695385,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -747989,11 +695431,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -748039,6 +695476,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748093,10 +695534,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -748144,11 +695581,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -748194,6 +695626,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748248,10 +695684,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -748298,11 +695730,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -748348,6 +695775,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748402,10 +695833,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -748452,11 +695879,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -748502,6 +695924,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748560,10 +695986,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -748615,11 +696037,6 @@
"state": "exact",
"version": "1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -748667,6 +696084,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748720,10 +696141,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -748761,16 +696178,16 @@
"versions": [
"3.7.0",
"3.7.0+galaxy1",
- "3.5.0.1",
- "3.6.0"
+ "3.6.0",
+ "3.5.0.1"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "3.17.0+galaxy1",
- "3.16.0+galaxy1"
+ "3.16.0+galaxy1",
+ "3.17.0+galaxy1"
]
},
{
@@ -748778,19 +696195,14 @@
"state": "exact",
"version": "3.14.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.14.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"3.12.0",
- "3.12.0+galaxy1",
+ "3.7.0+galaxy2",
"3.14.0+galaxy0",
- "3.7.0+galaxy2"
+ "3.12.0+galaxy1"
]
},
{
@@ -748833,6 +696245,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -748885,10 +696301,6 @@
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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"state": "exact",
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{
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"video_view": 0,
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],
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"Recognise the common issues and be able to resolve them"
],
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@@ -750796,138 +697930,6 @@
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"twitter": "bebatut",
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- "matrix": "hexylena:matrix.org",
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}
],
"dir": "topics/statistics/tutorials/classification_regression",
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],
"short_id": "T00263",
"short_tools": [
- "plotly_regression_performance_plots",
"sklearn_svm_classifier",
"plotly_ml_performance_plots",
+ "plotly_regression_performance_plots",
"sklearn_ensemble"
],
"slides": false,
@@ -751038,6 +698040,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -751093,10 +698099,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -751143,11 +698145,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -751192,6 +698189,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -751244,10 +698245,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -751291,10 +698288,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -751340,6 +698333,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -751392,10 +698389,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -751439,10 +698432,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -751488,6 +698477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -751540,10 +698533,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -751587,16 +698576,6 @@
"state": "exact",
"version": "1.0.8.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.8.4",
- "1.0.8.3",
- "1.0.10.0",
- "1.0.11.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -751642,6 +698621,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -751694,10 +698677,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -751741,16 +698720,6 @@
"state": "exact",
"version": "1.0.8.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.0.8.4",
- "1.0.10.0",
- "1.0.8.3",
- "1.0.11.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -751945,7 +698914,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nbreast-w_targets\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Support vector machines SVMs\"];\n 0 -->|output| 3;\n 0 -->|output| 3;\n 4[\"Support vector machines SVMs\"];\n 2 -->|output| 4;\n 3 -->|outfile_fit| 4;\n 5[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n 3 -->|outfile_fit| 5;\n 4 -->|outfile_predict| 5;\n 1 -->|output| 5;\n 0fac82f3-c1b2-482f-a31f-30b623a0f223[\"Output\\noutput_roc\"];\n 5 --> 0fac82f3-c1b2-482f-a31f-30b623a0f223;\n style 0fac82f3-c1b2-482f-a31f-30b623a0f223 stroke:#2c3143,stroke-width:4px;\n 431f3596-7b80-44f0-83ee-dda8c58e1e8c[\"Output\\noutput_confusion\"];\n 5 --> 431f3596-7b80-44f0-83ee-dda8c58e1e8c;\n style 431f3596-7b80-44f0-83ee-dda8c58e1e8c stroke:#2c3143,stroke-width:4px;\n ab62de11-fa69-4d59-9ebe-d5d0562f3c18[\"Output\\noutput_prf\"];\n 5 --> ab62de11-fa69-4d59-9ebe-d5d0562f3c18;\n style ab62de11-fa69-4d59-9ebe-d5d0562f3c18 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Classification LSVC",
"outputs": [
{
@@ -752311,7 +699280,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nbody_fat_test\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nbody_fat_train\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nbody_fat_test_labels\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Ensemble methods\"];\n 1 -->|output| 3;\n 1 -->|output| 3;\n 4[\"Ensemble methods\"];\n 0 -->|output| 4;\n 3 -->|outfile_fit| 4;\n 5[\"Plot actual vs predicted curves and residual plots\"];\n 4 -->|outfile_predict| 5;\n 2 -->|output| 5;\n cf1a5f94-f79d-4d13-b142-c3e20e25b658[\"Output\\noutput_scatter_plot\"];\n 5 --> cf1a5f94-f79d-4d13-b142-c3e20e25b658;\n style cf1a5f94-f79d-4d13-b142-c3e20e25b658 stroke:#2c3143,stroke-width:4px;\n e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a[\"Output\\noutput_actual_vs_pred\"];\n 5 --> e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a;\n style e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a stroke:#2c3143,stroke-width:4px;\n 2cbc04d3-d2d9-4623-b63d-51f1b024d611[\"Output\\noutput_residual_plot\"];\n 5 --> 2cbc04d3-d2d9-4623-b63d-51f1b024d611;\n style 2cbc04d3-d2d9-4623-b63d-51f1b024d611 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Regression GradientBoosting",
"outputs": [
{
@@ -752561,19 +699530,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/clustering_machinelearning/tutorial.json",
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- "reviewing": [
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- "bgruening",
- "anuprulez",
- "khanteymoori",
- "melpetera"
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"contributors": [
{
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@@ -752602,105 +699558,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
"twitter": "musafirtweetsz",
"url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
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- "elixir-europe"
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- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
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}
],
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@@ -752720,8 +699577,7 @@
"hands_on": true,
"id": "statistics/clustering_machinelearning",
"inexact_supported_servers": [
- "UseGalaxy.cz",
- "UseGalaxy.fr"
+ "UseGalaxy.cz"
],
"js_requirements": {
"mathjax": null,
@@ -752742,15 +699598,15 @@
"Apply clustering algorithms to different datasets",
"Learn how to visualize clusters"
],
- "pageviews": 13417,
+ "pageviews": 13427,
"pub_date": "2020-05-08",
"questions": [
"How to use clustering algorithms to categorize data in different clusters"
],
"short_id": "T00264",
"short_tools": [
- "sklearn_numeric_clustering",
"ggplot2_point",
+ "sklearn_numeric_clustering",
"csv_to_tabular"
],
"slides": false,
@@ -752788,11 +699644,6 @@
"name": "UseGalaxy.cz",
"url": "https://usegalaxy.cz/",
"usegalaxy": false
- },
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -752818,6 +699669,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -752873,10 +699728,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -752923,11 +699774,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -752972,6 +699818,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -753024,10 +699874,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -753068,10 +699914,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -753114,6 +699956,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -753166,10 +700012,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -753213,16 +700055,6 @@
"state": "exact",
"version": "1.0.8.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "1.0.8.3",
- "1.0.8.4",
- "1.0.11.0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -753268,6 +700100,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -753324,10 +700160,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -753376,11 +700208,6 @@
"state": "exact",
"version": "2.2.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -753433,7 +700260,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 57,
- "visitors": 7909,
+ "visitors": 7917,
"workflows": [
{
"creators": [],
@@ -753543,7 +700370,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\niris\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\ncircles\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Numeric Clustering\"];\n 2 -->|output| 10;\n 11[\"Numeric Clustering\"];\n 2 -->|output| 11;\n 12[\"Numeric Clustering\"];\n 3 -->|tabular| 12;\n 13[\"Numeric Clustering\"];\n 3 -->|tabular| 13;\n 14[\"Numeric Clustering\"];\n 3 -->|tabular| 14;\n 15[\"Scatterplot with ggplot2\"];\n 5 -->|outfile| 15;\n 275528af-4af3-4dc6-a958-737f4d2f89bd[\"Output\\nheirarchical_clustering_circles\"];\n 15 --> 275528af-4af3-4dc6-a958-737f4d2f89bd;\n style 275528af-4af3-4dc6-a958-737f4d2f89bd stroke:#2c3143,stroke-width:4px;\n 16[\"Scatterplot with ggplot2\"];\n 6 -->|outfile| 16;\n 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9[\"Output\\nkmeans_clustering_circles\"];\n 16 --> 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9;\n style 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9 stroke:#2c3143,stroke-width:4px;\n 17[\"Scatterplot with ggplot2\"];\n 7 -->|outfile| 17;\n 9664ba05-4664-4ceb-8f93-0974b20bf9e1[\"Output\\ndbscan_clustering_circles\"];\n 17 --> 9664ba05-4664-4ceb-8f93-0974b20bf9e1;\n style 9664ba05-4664-4ceb-8f93-0974b20bf9e1 stroke:#2c3143,stroke-width:4px;\n 18[\"Scatterplot with ggplot2\"];\n 9 -->|outfile| 18;\n d82a4483-7f38-4614-96b4-2a9b3316c808[\"Output\\nheirarchical_clustering_moon\"];\n 18 --> d82a4483-7f38-4614-96b4-2a9b3316c808;\n style d82a4483-7f38-4614-96b4-2a9b3316c808 stroke:#2c3143,stroke-width:4px;\n 19[\"Scatterplot with ggplot2\"];\n 10 -->|outfile| 19;\n 00c0ca58-4ee5-4606-8c1b-c172431e5dbd[\"Output\\ndbscan_clustering_moon\"];\n 19 --> 00c0ca58-4ee5-4606-8c1b-c172431e5dbd;\n style 00c0ca58-4ee5-4606-8c1b-c172431e5dbd stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nmoon\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 20[\"Scatterplot with ggplot2\"];\n 11 -->|outfile| 20;\n 5717bf22-83e3-46a2-8f6d-12a1fa41439b[\"Output\\nkmeans_clustering_moon\"];\n 20 --> 5717bf22-83e3-46a2-8f6d-12a1fa41439b;\n style 5717bf22-83e3-46a2-8f6d-12a1fa41439b stroke:#2c3143,stroke-width:4px;\n 21[\"Scatterplot with ggplot2\"];\n 12 -->|outfile| 21;\n 0ace8714-ff3a-4efd-a649-70924b1e6230[\"Output\\nheirarchical_clustering_iris\"];\n 21 --> 0ace8714-ff3a-4efd-a649-70924b1e6230;\n style 0ace8714-ff3a-4efd-a649-70924b1e6230 stroke:#2c3143,stroke-width:4px;\n 22[\"Scatterplot with ggplot2\"];\n 13 -->|outfile| 22;\n e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd[\"Output\\nkmeans_clustering_iris\"];\n 22 --> e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd;\n style e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd stroke:#2c3143,stroke-width:4px;\n 23[\"Scatterplot with ggplot2\"];\n 14 -->|outfile| 23;\n 119d1cde-567a-47f0-99de-00d3557c38a2[\"Output\\ndbscan_clustering_iris\"];\n 23 --> 119d1cde-567a-47f0-99de-00d3557c38a2;\n style 119d1cde-567a-47f0-99de-00d3557c38a2 stroke:#2c3143,stroke-width:4px;\n 3[\"Convert CSV to tabular\"];\n 0 -->|output| 3;\n 4[\"Scatterplot with ggplot2\"];\n 1 -->|output| 4;\n 5[\"Numeric Clustering\"];\n 1 -->|output| 5;\n 6[\"Numeric Clustering\"];\n 1 -->|output| 6;\n 7[\"Numeric Clustering\"];\n 1 -->|output| 7;\n 8[\"Scatterplot with ggplot2\"];\n 2 -->|output| 8;\n 9[\"Numeric Clustering\"];\n 2 -->|output| 9;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Clustering in Machine Learning",
"outputs": [
{
@@ -754024,21 +700851,6 @@
},
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@@ -754047,161 +700859,6 @@
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@@ -754232,7 +700889,7 @@
"Learn how to create a CNN using Galaxy's deep learning tools",
"Solve an image classification problem on MNIST digit classification dataset using CNN in Galaxy"
],
- "pageviews": 5646100,
+ "pageviews": 5668918,
"pub_date": "2021-04-19",
"questions": [
"What is a convolutional neural network (CNN)?",
@@ -754278,11 +700935,11 @@
],
"short_id": "T00257",
"short_tools": [
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"keras_model_builder",
+ "ml_visualization_ex",
+ "keras_model_config",
"model_prediction",
"sklearn_to_categorical",
- "keras_model_config",
"keras_train_and_eval"
],
"slides": true,
@@ -754335,6 +700992,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -754390,10 +701051,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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"url": "https://usegalaxy.eu",
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"url": "https://usegalaxy.no/",
@@ -754489,6 +701141,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"state": "missing"
@@ -755439,7 +702067,7 @@
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"video_view": 0,
"visit_duration": 206,
- "visitors": 2094789,
+ "visitors": 2104837,
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@@ -755585,7 +702213,7 @@
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+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Intro_To_CNN_v1.0.11.0",
"outputs": [],
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@@ -755661,18 +702289,6 @@
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- "natefoo"
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@@ -755681,102 +702297,6 @@
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@@ -755819,7 +702339,7 @@
"Learn how to create a neural network using Galaxy's deep learning tools",
"Solve a simple regression problem, car purchase price prediction, via FNN in Galaxy"
],
- "pageviews": 5633838,
+ "pageviews": 5656697,
"pub_date": "2021-04-28",
"questions": [
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@@ -755850,10 +702370,10 @@
],
"short_id": "T00258",
"short_tools": [
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"keras_model_builder",
- "model_prediction",
"keras_model_config",
+ "model_prediction",
+ "plotly_regression_performance_plots",
"keras_train_and_eval"
],
"slides": true,
@@ -755916,6 +702436,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -755971,10 +702495,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -756021,11 +702541,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -756070,6 +702585,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
"state": "missing"
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"state": "exact",
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{
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"state": "inexact",
@@ -756223,6 +702734,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -756275,10 +702790,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -756325,10 +702836,6 @@
"state": "exact",
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -756377,6 +702884,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -756429,10 +702940,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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"state": "missing"
@@ -756479,10 +702986,6 @@
"state": "exact",
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},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -756533,6 +703036,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -756585,10 +703092,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -756634,17 +703137,13 @@
"state": "exact",
"version": "1.0.10.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.0.8.2",
- "1.0.8.1",
"1.0.8.4",
+ "1.0.8.1",
"1.0.8.3"
]
},
@@ -756688,6 +703187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -756740,10 +703243,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -756787,10 +703286,6 @@
"state": "exact",
"version": "0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -756845,7 +703340,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 198,
- "visitors": 2098204,
+ "visitors": 2108296,
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{
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@@ -756984,7 +703479,7 @@
],
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"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Create a deep learning model architecture\"];\n 5[\"Create deep learning model\"];\n 4 -->|outfile| 5;\n 6[\"Deep learning training and evaluation\"];\n 5 -->|outfile| 6;\n 1 -->|output| 6;\n 3 -->|output| 6;\n 7[\"Model Prediction\"];\n 6 -->|outfile_object| 7;\n 0 -->|output| 7;\n 8[\"Plot actual vs predicted curves and residual plots\"];\n 2 -->|output| 8;\n 7 -->|outfile_predict| 8;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Intro_To_FNN_v1_0_10_0",
"outputs": [],
"parent_id": "statistics/FNN",
@@ -757049,24 +703544,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json",
- "contributions": {
- "authorship": [
- "marziacremona",
- "cumbof"
- ],
- "reviewing": [
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- "shiltemann",
- "nsoranzo",
- "bgruening",
- "bedroesb",
- "dsobral",
- "hexylena",
- "lecorguille",
- "cumbof",
- "njall"
- ]
- },
"contributors": [
{
"email": "mac78@psu.edu",
@@ -757086,202 +703563,15 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/cumbof/",
"twitter": "cumbofabio",
"url": "https://training.galaxyproject.org/training-material/api/contributors/cumbof.json"
- },
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- "contact_for_training": true,
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- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
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- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
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- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
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- "contact_for_training": true,
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- "fediverse": "https://mstdn.science/@shiltemann",
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- "email": "fabio.cumbo@gmail.com",
- "id": "cumbof",
- "joined": "2018-02",
- "linkedin": "fabiocumbo",
- "name": "Fabio Cumbo",
- "orcid": "0000-0003-2920-5838",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cumbof/",
- "twitter": "cumbofabio",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/cumbof.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/statistics/tutorials/iwtomics",
"edam_operation": [
"Peak calling",
+ "Genome annotation",
"Comparison",
"Differential gene expression analysis",
- "Differentially-methylated region identification",
- "Genome annotation"
+ "Differentially-methylated region identification"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -757329,8 +703619,8 @@
"short_id": "T00269",
"short_tools": [
"iwtomics_testandplot",
- "iwtomics_loadandplot",
- "iwtomics_plotwithscale"
+ "iwtomics_plotwithscale",
+ "iwtomics_loadandplot"
],
"slides": false,
"slides_recordings": false,
@@ -757391,6 +703681,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -757446,10 +703740,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -757496,11 +703786,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -757545,6 +703830,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -757597,10 +703886,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -757644,10 +703929,6 @@
"state": "exact",
"version": "1.0.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -757694,151 +703975,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.0.0.0"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "1.0.0.0"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -757893,10 +704030,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -757941,9 +704074,149 @@
"version": "1.0.0.0"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.0.0.0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
"state": "missing"
},
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.0.0.0"
+ },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -758186,7 +704459,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nETn_fixed.bed\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nControl.bed\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nfeatures_header.tabular\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nregions_header.tabular\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nRecombination_hotspots.txt\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"IWTomics Load\"];\n 4 -->|output| 5;\n 2 -->|output| 5;\n 0 -->|output| 5;\n 1 -->|output| 5;\n 3 -->|output| 5;\n 6[\"IWTomics Test\"];\n 5 -->|outfeatures| 6;\n 5 -->|outrdata| 6;\n 5 -->|outregions| 6;\n 7[\"IWTomics Plot with Threshold\"];\n 6 -->|iwtomicsselectedfeatures| 7;\n 6 -->|iwtomicsrdata| 7;\n 6 -->|iwtomicstests| 7;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Workflow Constructed From History 'IWTomics Workflow'",
"outputs": [],
"parent_id": "statistics/iwtomics",
@@ -758242,20 +704515,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pmids_to_pubtator_matrix\n owner: iuc\n revisions: 69714f06f18b\n tool_panel_section_label: Other Tools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pubmed_by_queries\n owner: iuc\n revisions: 02e46a96e98a\n tool_panel_section_label: Other Tools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/text-mining_simtext/tutorial.json",
- "contributions": {
- "authorship": [
- "mgramm1",
- "dlalgroup",
- "blankenberg"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "dlal-group",
- "bgruening",
- "martenson"
- ]
- },
"contributors": [
{
"email": "mgramm2@smail.uni-koeln.de",
@@ -758282,127 +704541,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
"twitter": "dblankenberg",
"url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "id": "dlal-group",
- "name": "dlal-group",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dlal-group/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/dlal-group.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
- "id": "martenson",
- "joined": "2017-09",
- "location": {
- "country": "USA",
- "lat": 37.0,
- "lon": -122.0
- },
- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
}
],
"dir": "topics/statistics/tutorials/text-mining_simtext",
@@ -758435,7 +704573,7 @@
"Extract biomedical terms from the PubMed data for each biomedical entity",
"Analyze the similarity among the biomedical entities based on the extracted data in an interactive app"
],
- "pageviews": 576,
+ "pageviews": 577,
"pub_date": "2021-04-05",
"questions": [
"How can I automatically collect PubMed data for a set of biomedical entities such as genes?",
@@ -758443,9 +704581,9 @@
],
"short_id": "T00272",
"short_tools": [
+ "pubmed_by_queries",
"interactive_tool_simtext_app",
- "pmids_to_pubtator_matrix",
- "pubmed_by_queries"
+ "pmids_to_pubtator_matrix"
],
"slides": false,
"slides_recordings": false,
@@ -758481,6 +704619,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -758536,10 +704678,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -758586,11 +704724,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -758635,6 +704768,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -758687,10 +704824,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -758731,10 +704864,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -758777,6 +704906,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -758829,10 +704962,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -758875,10 +705004,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -758922,6 +705047,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -758974,10 +705103,6 @@
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],
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@@ -762336,13 +708185,13 @@
],
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"short_tools": [
- "ml_visualization_ex",
- "tp_cut_tool",
"keras_model_builder",
+ "ml_visualization_ex",
+ "keras_model_config",
"model_prediction",
"sklearn_to_categorical",
- "keras_model_config",
- "keras_train_and_eval"
+ "keras_train_and_eval",
+ "tp_cut_tool"
],
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"slides_recordings": false,
@@ -762393,6 +708242,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -762448,10 +708301,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -762498,11 +708347,6 @@
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- "url": "https://usegalaxy.fr/",
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"state": "exact",
@@ -762695,6 +708535,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "exact",
@@ -762843,6 +708679,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -762895,10 +708735,6 @@
"server": "http://galaxy.interactomix.com/",
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"state": "exact",
@@ -762991,6 +708823,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763043,10 +708879,6 @@
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- "state": "missing"
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{
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"state": "exact",
@@ -763142,6 +708970,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763194,10 +709026,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
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"state": "missing"
@@ -763241,10 +709069,6 @@
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- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -763290,6 +709114,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763342,10 +709170,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"state": "exact",
@@ -763440,6 +709260,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763492,10 +709316,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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{
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"state": "exact",
@@ -763588,6 +709404,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763640,10 +709460,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -763689,10 +709505,6 @@
"state": "exact",
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- "state": "missing"
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{
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"state": "exact",
@@ -763738,6 +709550,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763790,10 +709606,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
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"state": "missing"
@@ -763836,10 +709648,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -763884,6 +709692,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -763938,10 +709750,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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{
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"state": "inexact",
@@ -763989,11 +709797,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "1.1.0"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -764053,7 +709856,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 195,
- "visitors": 1754988,
+ "visitors": 1765051,
"workflows": [
{
"creators": [
@@ -764263,7 +710066,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ntest_y_10.tsv\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\ntrain_y_10.tsv\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ntrain_X_10.tsv\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\ntest_X_10.tsv\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Create a deep learning model architecture\"];\n 5[\"Advanced Cut\"];\n 0 -->|output| 5;\n 6[\"Advanced Cut\"];\n 1 -->|output| 6;\n 7[\"Create deep learning model\"];\n 4 -->|outfile| 7;\n 8[\"To categorical\"];\n 6 -->|output| 8;\n 9[\"Deep learning training and evaluation\"];\n 7 -->|outfile| 9;\n 2 -->|output| 9;\n 8 -->|outfile| 9;\n 10[\"Model Prediction\"];\n 9 -->|outfile_object| 10;\n 9 -->|outfile_weights| 10;\n 3 -->|output| 10;\n 11[\"Machine Learning Visualization Extension\"];\n 10 -->|outfile_predict| 11;\n 5 -->|output| 11;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "fruit_360",
"outputs": [
{
@@ -764973,18 +710776,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: plotly_parallel_coordinates_plot\n owner: bgruening\n revisions: 7b21a9b5922f\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_regression_performance_plots\n owner: bgruening\n revisions: 389227fa1864\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_build_pipeline\n owner: bgruening\n revisions: 840f29aad145\n tool_panel_section_label: Machine Learning\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_ensemble\n owner: bgruening\n revisions: 1a53edc4b438\n tool_panel_section_label: Machine Learning\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_searchcv\n owner: bgruening\n revisions: 25ab6b4e376e\n tool_panel_section_label: Machine Learning\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "anuprulez"
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- "reviewing": [
- "shiltemann",
- "bebatut",
- "bgruening",
- "khanteymoori"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -765010,109 +710801,6 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
"twitter": "musafirtweetsz",
"url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
- },
- {
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
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- "former_affiliations": [
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- "elixir-europe"
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- "id": "khanteymoori",
- "joined": "2019-07",
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- "orcid": "0000-0001-6811-9196",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khanteymoori/",
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}
],
"dir": "topics/statistics/tutorials/age-prediction-with-ml",
@@ -765149,18 +710837,18 @@
"Apply regression based machine learning algorithms",
"Learn feature selection and hyperparameter optimisation"
],
- "pageviews": 20673,
+ "pageviews": 20685,
"pub_date": "2019-01-25",
"questions": [
"How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?"
],
"short_id": "T00261",
"short_tools": [
+ "plotly_parallel_coordinates_plot",
"plotly_regression_performance_plots",
"sklearn_build_pipeline",
- "plotly_parallel_coordinates_plot",
- "sklearn_searchcv",
- "sklearn_ensemble"
+ "sklearn_ensemble",
+ "sklearn_searchcv"
],
"slides": false,
"slides_recordings": false,
@@ -765222,6 +710910,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -765277,10 +710969,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -765327,11 +711015,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -765376,6 +711059,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -765428,10 +711115,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -765475,10 +711158,6 @@
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{
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"state": "exact",
@@ -765524,6 +711203,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -765576,10 +711259,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -765623,10 +711302,6 @@
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -765672,6 +711347,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -765724,10 +711403,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
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{
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"state": "missing"
@@ -765771,16 +711446,6 @@
"state": "exact",
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},
- {
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- "state": "inexact",
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@@ -766146,7 +711791,7 @@
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@@ -766301,7 +711946,7 @@
],
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- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Age Prediction DNA Methylation",
"outputs": [
{
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],
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+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Age Prediction RNA-Seq",
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@@ -767091,112 +712723,6 @@
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@@ -767233,7 +712759,7 @@
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"Learn how visualizations can be used to analyze predictions"
],
- "pageviews": 3519,
+ "pageviews": 3526,
"pub_date": "2020-01-25",
"questions": [
"How to use regression techniques to create predictive models from biological datasets?"
@@ -767255,11 +712781,11 @@
"short_id": "T00271",
"short_tools": [
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- "sklearn_generalized_linear",
"sklearn_build_pipeline",
"Remove beginning1",
- "sklearn_searchcv",
- "sklearn_ensemble"
+ "sklearn_generalized_linear",
+ "sklearn_ensemble",
+ "sklearn_searchcv"
],
"slides": false,
"slides_recordings": false,
@@ -767321,6 +712847,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -767426,11 +712952,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -767475,6 +712996,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -767527,10 +713052,6 @@
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{
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@@ -767571,10 +713092,6 @@
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{
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"state": "local"
@@ -767617,6 +713134,10 @@
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{
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"state": "missing"
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{
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"state": "exact",
@@ -767765,6 +713278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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@@ -767853,25 +713366,25 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
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"1.0.8.2",
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{
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"state": "inexact",
"versions": [
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"1.0.0.4",
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+ "1.0.8.1",
+ "1.0.10.0",
"1.0.7.10",
- "1.0.8.3",
"1.0",
- "1.0.10.0",
- "0.9",
+ "1.0.7.12",
"1.0.8.4",
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"state": "inexact",
@@ -767932,6 +713440,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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@@ -767984,10 +713496,6 @@
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{
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@@ -768021,8 +713529,8 @@
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- "1.0.7.12",
"1.0.8.2",
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"1.0.8.3",
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"1.0.8.2",
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]
},
{
@@ -768101,6 +713604,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -768153,10 +713660,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
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"state": "missing"
@@ -768189,23 +713692,23 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.0.8.2",
- "1.0.8.1"
+ "1.0.8.1",
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"state": "inexact",
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"1.0.8.1",
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"1.0.8.4",
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- "0.9",
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"1.0.8.3",
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@@ -768214,17 +713717,12 @@
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"versions": [
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"1.0.8.1",
+ "1.0.8.2",
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]
@@ -768269,6 +713767,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -768321,10 +713823,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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"state": "missing"
@@ -768357,8 +713855,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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"1.0.8.1",
+ "1.0.8.2",
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]
},
@@ -768366,16 +713864,16 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
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"1.0.8.1",
+ "1.0.8.2",
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+ "0.9",
+ "1.0.7.10",
"1.0.8.3",
"1.0",
- "1.0.7.10",
- "0.9",
- "1.0.0.4"
+ "1.0.10.0",
+ "1.0.0.4",
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]
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@@ -768383,19 +713881,14 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.11.0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.0.8.2",
"1.0.8.1",
- "1.0.8.4",
- "1.0.8.3"
+ "1.0.8.2",
+ "1.0.8.3",
+ "1.0.8.4"
]
},
{
@@ -768448,7 +713941,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 67,
- "visitors": 2829,
+ "visitors": 2835,
"workflows": [
{
"creators": [
@@ -768560,7 +714053,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\ntrain_rows\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ntest_rows\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Pipeline Builder\"];\n 4[\"Generalized linear models\"];\n 0 -->|output| 4;\n 0 -->|output| 4;\n 5[\"Ensemble methods\"];\n 0 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Remove beginning\"];\n 1 -->|output| 6;\n 7[\"Hyperparameter Search\"];\n 3 -->|outfile| 7;\n 0 -->|output| 7;\n 0 -->|output| 7;\n 8[\"Generalized linear models\"];\n 2 -->|output| 8;\n 4 -->|outfile_fit| 8;\n 9[\"Ensemble methods\"];\n 2 -->|output| 9;\n 5 -->|outfile_fit| 9;\n 10[\"Ensemble methods\"];\n 2 -->|output| 10;\n 7 -->|outfile_object| 10;\n 11[\"Plot actual vs predicted curves and residual plots\"];\n 6 -->|out_file1| 11;\n 8 -->|outfile_predict| 11;\n 12[\"Plot actual vs predicted curves and residual plots\"];\n 1 -->|output| 12;\n 9 -->|outfile_predict| 12;\n 13[\"Plot actual vs predicted curves and residual plots\"];\n 1 -->|output| 13;\n 10 -->|outfile_predict| 13;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "ml_regression",
"outputs": [],
"parent_id": "statistics/regression_machinelearning",
@@ -768612,165 +714105,7 @@
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- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
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{
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@@ -768802,9 +714137,7 @@
"feedback_number": 0,
"hands_on": true,
"id": "statistics/machinelearning",
- "inexact_supported_servers": [
- "UseGalaxy.fr"
- ],
+ "inexact_supported_servers": [],
"js_requirements": {
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"mermaid": false
@@ -768825,7 +714158,7 @@
"Learn how to do classification using the training and test data.",
"Learn how to use Galaxy's machine learning tools."
],
- "pageviews": 2901,
+ "pageviews": 2909,
"pub_date": "2018-11-05",
"questions": [
"What is machine learning?",
@@ -768872,13 +714205,7 @@
"usegalaxy": true
}
],
- "inexact": [
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- }
- ]
+ "inexact": []
},
"supported_servers_matrix": {
"servers": [
@@ -768902,6 +714229,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -768957,10 +714288,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -769007,11 +714334,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -769056,6 +714378,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -769108,10 +714434,6 @@
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"state": "missing"
},
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- "state": "missing"
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{
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@@ -769155,16 +714477,6 @@
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{
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"state": "exact",
@@ -769215,7 +714527,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 175,
- "visitors": 2097,
+ "visitors": 2104,
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@@ -769320,7 +714632,7 @@
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- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Machine Learning",
"outputs": [
{
@@ -769909,19 +715221,7 @@
"tools": []
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
- "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/galaxy-ludwig/tutorial.json",
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- "jgoecks"
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- "reviewing": [
- "shiltemann",
- "paulocilasjr",
- "anuprulez"
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+ "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/loris_model/tutorial.json",
"contributors": [
{
"affiliations": [
@@ -769958,40 +715258,706 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/jgoecks/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/jgoecks.json"
- },
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+ "edam_topic": [],
+ "exact_supported_servers": [],
+ "feedback_mean_note": null,
+ "feedback_number": 0,
+ "hands_on": true,
+ "id": "statistics/loris_model",
+ "inexact_supported_servers": [],
+ "js_requirements": {
+ "mathjax": null,
+ "mermaid": false
+ },
+ "key_points": [
+ "Use Galaxy tools to build a model based on LORIS Score model published (Chang et al., 2024).",
+ "Confirm the robustness of the model by comparing its metrics with the model published by Chang et al., 2024."
+ ],
+ "layout": "tutorial_hands_on",
+ "level": "Intermediate",
+ "license": "CC-BY-4.0",
+ "mod_date": "2024-12-13",
+ "objectives": [
+ "Use a large dataset of immune checkpoint blockade (ICB)-treated and non-ICB-treated patients across 18 solid tumor types, encompassing a wide range of clinical, pathologic and genomic features to build a Machine Learning Model.",
+ "Build a Machine Learning model using PyCaret in Galaxy.",
+ "Evaluate the model for robustness by comparing it with the original LORIS LLR6 model published by Chang et al., 2024."
+ ],
+ "pageviews": 5,
+ "pub_date": "2024-12-13",
+ "questions": [
+ "How can the LORIS LLR6 model published by Chang et al., 2024 be reproduced?",
+ "Which tools can be used in Galaxy to obtain a logistic regression model?",
+ "How can the model be evaluated to confirm its performance?"
+ ],
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+ "short_tools": [
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],
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+ "ml_visualization_ex",
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],
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{
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{
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"versions": [
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"1.0.8.1",
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+ "1.0.8.3",
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]
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+ "state": "missing"
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{
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{
@@ -772899,6 +718450,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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"state": "missing"
@@ -772951,10 +718506,6 @@
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{
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 81,
- "visitors": 950,
+ "visit_duration": 80,
+ "visitors": 955,
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@@ -773159,7 +718706,7 @@
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+ "modified": "2024-12-13 13:26:19 +0000",
"name": "gpu_jupytool",
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@@ -773435,81 +718971,6 @@
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
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"dir": "topics/statistics/tutorials/intro_deep_learning",
@@ -773545,7 +719006,7 @@
"Learn about Galaxy deep learning tools",
"Learn how to interpret predictions"
],
- "pageviews": 2588,
+ "pageviews": 2599,
"pub_date": "2020-03-26",
"questions": [
"What are deep learning and neural networks?",
@@ -773554,10 +719015,10 @@
],
"short_id": "T00268",
"short_tools": [
- "ml_visualization_ex",
"keras_model_builder",
- "model_prediction",
+ "ml_visualization_ex",
"keras_model_config",
+ "model_prediction",
"keras_train_and_eval"
],
"slides": false,
@@ -773619,6 +719080,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -773674,10 +719139,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -773724,11 +719185,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -773773,6 +719229,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -773825,10 +719285,6 @@
"server": "http://galaxy.interactomix.com/",
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},
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -773872,10 +719328,6 @@
"state": "exact",
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},
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- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -773921,6 +719373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -773973,10 +719429,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -774020,10 +719472,6 @@
"state": "exact",
"version": "0.5.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -774069,6 +719517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -774121,10 +719573,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -774168,10 +719616,6 @@
"state": "exact",
"version": "1.0.8.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -774217,6 +719661,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -774269,10 +719717,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -774316,10 +719760,6 @@
"state": "exact",
"version": "1.0.8.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -774365,6 +719805,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -774417,10 +719861,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -774464,10 +719904,6 @@
"state": "exact",
"version": "1.0.8.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -774521,8 +719957,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 100,
- "visitors": 2007,
+ "visit_duration": 99,
+ "visitors": 2014,
"workflows": [
{
"creators": [],
@@ -774672,7 +720108,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Create a deep learning model architecture\"];\n 5[\"Create deep learning model\"];\n 4 -->|outfile| 5;\n 6[\"Deep learning training and evaluation\"];\n 5 -->|outfile| 6;\n 1 -->|output| 6;\n 3 -->|output| 6;\n 7[\"Model Prediction\"];\n 6 -->|outfile_object| 7;\n 6 -->|outfile_weights| 7;\n 0 -->|output| 7;\n 8[\"Machine Learning Visualization Extension\"];\n 7 -->|outfile_predict| 8;\n 2 -->|output| 8;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Intro_To_Deep_Learning",
"outputs": [],
"parent_id": "statistics/intro_deep_learning",
@@ -774765,22 +720201,6 @@
},
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- "anuprulez",
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- "reviewing": [
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- "shiltemann",
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- "hexylena",
- "anuprulez",
- "khanteymoori",
- "simonbray"
- ]
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"contributors": [
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@@ -774810,150 +720230,6 @@
"twitter": "musafirtweetsz",
"url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
},
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- "elixir-europe"
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- "id": "simonbray",
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- "elixir-europe"
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- "id": "teresa-m",
- "joined": "2022-09",
- "name": "Teresa M\u00fcller",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
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- "contact_for_training": true,
- "elixir_node": "nl",
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- "fediverse": "https://mstdn.science/@shiltemann",
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- "gallantries",
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "contact_for_training": true,
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- "fediverse": "https://fosstodon.org/@bgruening",
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- "linkedin": "bgruening",
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- "elixir_node": "de",
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- "former_affiliations": [
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/khanteymoori.json"
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{
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"former_affiliations": [
@@ -775004,7 +720280,7 @@
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"Learn how visualizations can be used to analyze the classification results"
],
- "pageviews": 3446,
+ "pageviews": 3461,
"pub_date": "2020-04-30",
"questions": [
"What is classification and how we can use classification techniques?"
@@ -775038,14 +720314,14 @@
],
"short_id": "T00262",
"short_tools": [
+ "plotly_ml_performance_plots",
+ "sklearn_svm_classifier",
"sklearn_build_pipeline",
- "sklearn_generalized_linear",
"Remove beginning1",
- "sklearn_svm_classifier",
+ "sklearn_generalized_linear",
"sklearn_nn_classifier",
- "sklearn_searchcv",
- "plotly_ml_performance_plots",
- "sklearn_ensemble"
+ "sklearn_ensemble",
+ "sklearn_searchcv"
],
"slides": false,
"slides_recordings": false,
@@ -775107,6 +720383,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -775162,10 +720442,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -775212,11 +720488,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -775261,6 +720532,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -775313,10 +720588,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -775357,10 +720628,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -775403,6 +720670,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -775455,10 +720726,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -775508,10 +720775,6 @@
"state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -775560,6 +720823,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -775612,10 +720879,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -775648,25 +720911,25 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.0.8.1",
+ "1.0.0.4",
"1.0.8.2",
- "1.0.0.4"
+ "1.0.8.1"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.0.8.1",
- "1.0.8.2",
"1.0.0.4",
+ "1.0.8.2",
+ "1.0.8.1",
+ "1.0.10.0",
"1.0.7.10",
- "1.0.8.3",
"1.0",
- "1.0.10.0",
- "0.9",
+ "1.0.7.12",
"1.0.8.4",
- "1.0.7.12"
+ "0.9",
+ "1.0.8.3"
]
},
{
@@ -775674,11 +720937,6 @@
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{
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@@ -775728,172 +720986,7 @@
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"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "visit_duration": 120,
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],
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@@ -778245,6 +723225,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"url": "https://mississippi.sorbonne-universite.fr",
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"url": "https://usegalaxy.eu",
"usegalaxy": true
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -778399,6 +723374,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -778451,10 +723430,6 @@
"server": "http://galaxy.interactomix.com/",
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@@ -778495,10 +723470,6 @@
"server": "https://usegalaxy.eu",
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@@ -778547,7 +723518,7 @@
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],
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@@ -778763,7 +723648,7 @@
"Compute the global score for the previous annotated pathways.",
"Rank the computed heterologous pathways depending on their score."
],
- "pageviews": 683,
+ "pageviews": 688,
"pub_date": "2022-09-26",
"questions": [
"How to evaluate a set of heterologous pathways ?"
@@ -778784,9 +723669,9 @@
],
"short_id": "T00274",
"short_tools": [
- "rpthermo",
"rpfba",
"rpscore",
+ "rpthermo",
"rpranker"
],
"slides": false,
@@ -778817,6 +723702,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -778872,10 +723761,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -778922,11 +723807,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -778971,6 +723851,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -779023,10 +723907,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -779067,10 +723947,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -779113,6 +723989,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -779165,10 +724045,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -779209,10 +724085,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -779255,6 +724127,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -779307,10 +724183,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -779351,10 +724223,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -779397,6 +724265,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -779449,10 +724321,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -779493,10 +724361,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -779546,8 +724410,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 211,
- "visitors": 433,
+ "visit_duration": 213,
+ "visitors": 437,
"workflows": [
{
"creators": [],
@@ -779707,7 +724571,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nHeterologous pathways\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nChassis where to produce target from\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nCell compartment ID\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nBiomass reaction ID\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"Flux balance analysis\"];\n 3 -->|output| 4;\n 2 -->|output| 4;\n 1 -->|output| 4;\n 0 -->|output| 4;\n 5[\"Thermo\"];\n 4 -->|pathway_with_fba| 5;\n 6[\"Score Pathway\"];\n 5 -->|pathway_with_thermo| 6;\n 7[\"Rank Pathways\"];\n 6 -->|scored_pathway| 7;\n 8111f525-5845-4ac2-a1d6-c4bfd218cf3f[\"Output\\nRanked Pathways\"];\n 7 --> 8111f525-5845-4ac2-a1d6-c4bfd218cf3f;\n style 8111f525-5845-4ac2-a1d6-c4bfd218cf3f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:36 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Pathway Analysis",
"outputs": [
{
@@ -779996,21 +724860,6 @@
},
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"Generate dnabot scripts enabling the automatic build of plasmids."
],
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"pub_date": "2022-05-12",
"questions": [
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@@ -780198,8 +724976,8 @@
"short_id": "T00273",
"short_tools": [
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- "dnabot",
- "rpbasicdesign"
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"slides_recordings": false,
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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"video_versions": 1,
"video_view": 0,
- "visit_duration": 143,
- "visitors": 754,
+ "visit_duration": 142,
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],
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"twitter": "jeanloupfaulon",
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- "bio": "Researcher at Erasmus Medical Center",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/synthetic-biology/tutorials/retrosynthesis_analysis",
@@ -781487,7 +726188,7 @@
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"Understanding how to run the tools to search heterologous pathways."
],
- "pageviews": 549,
+ "pageviews": 550,
"pub_date": "2022-06-23",
"questions": [
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@@ -781508,12 +726209,12 @@
],
"short_id": "T00275",
"short_tools": [
- "rpcompletion",
- "rpextractsink",
"rrparser",
+ "retropath2",
"get_sbml_model",
- "rp2paths",
- "retropath2"
+ "rpcompletion",
+ "rpextractsink",
+ "rp2paths"
],
"slides": false,
"slides_recordings": false,
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"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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{
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"url": "https://mississippi.sorbonne-universite.fr",
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{
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"url": "https://usegalaxy.no/",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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- "visit_duration": 139,
- "visitors": 375,
+ "visit_duration": 138,
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"What should we think about when we organize a workshop?",
@@ -786583,7 +730637,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 59,
- "visitors": 166
+ "visitors": 167
},
{
"admin_install": {
@@ -786594,20 +730648,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json",
- "contributions": {
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- ],
- "reviewing": [
- "bgruening",
- "hexylena",
- "shiltemann",
- "bebatut",
- "abretaud",
- "nsoranzo",
- "martenson"
- ]
- },
"contributors": [
{
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@@ -786637,190 +730677,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "joined": "2017-09",
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- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "by-covid",
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- "elixir-converge"
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- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
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- "contact_for_training": true,
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- "linkedin": "berenicebatut",
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- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
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- "contact_for_training": true,
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- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
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- "matrix": "abretaud:matrix.org",
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- "twitter": "abretau",
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- "matrix": "nsoranzo:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "contact_for_training": true,
- "elixir_node": "cz",
- "email": "marten@bx.psu.edu",
- "fediverse": "https://mastodon.world/@martenson",
- "fediverse_flavor": "mastodon",
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- "lat": 37.0,
- "lon": -122.0
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- "matrix": "martenson:matrix.org",
- "name": "Martin \u010cech",
- "orcid": "0000-0002-9318-1781",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
}
],
"dir": "topics/teaching/tutorials/galaxy-admin-training",
@@ -786911,21 +730767,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json",
- "contributions": {
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- "bgruening",
- "shiltemann",
- "hexylena"
- ],
- "reviewing": [
- "hexylena",
- "abretaud",
- "shiltemann",
- "nsoranzo",
- "bgruening"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -787045,142 +730886,6 @@
"orcid": "0000-0001-9760-8992",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
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- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
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- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
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- "nfdi4plants",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
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- "deNBI",
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- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
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@@ -787202,7 +730907,7 @@
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"mod_date": "2023-11-09",
"objectives": null,
- "pageviews": 213,
+ "pageviews": 214,
"pub_date": "2018-11-15",
"questions": null,
"redirect_from": [
@@ -787241,7 +730946,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 42,
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+ "visitors": 93
},
{
"admin_install": {
@@ -787990,23 +731695,23 @@
],
"dir": "topics/transcriptomics/tutorials/differential-isoform-expression",
"edam_operation": [
+ "Validation",
"Visualisation",
- "Data handling",
- "Protein sequence analysis",
- "Statistical calculation",
"RNA-Seq analysis",
- "Sequencing quality control",
- "Formatting",
- "Sequence annotation",
- "Sequence alignment",
- "De-novo assembly",
- "Validation",
"Sequence assembly validation",
- "Sequence analysis",
- "Sequence composition calculation",
+ "Sequence annotation",
"Sequence comparison",
"Transcriptome assembly",
- "Sequence contamination filtering"
+ "Statistical calculation",
+ "Sequencing quality control",
+ "Sequence composition calculation",
+ "Data handling",
+ "Formatting",
+ "Sequence contamination filtering",
+ "Protein sequence analysis",
+ "Sequence analysis",
+ "Sequence alignment",
+ "De-novo assembly"
],
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"exact_supported_servers": [],
@@ -788017,7 +731722,6 @@
"inexact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"js_requirements": {
@@ -788037,7 +731741,7 @@
"Perform genome-wide isoform analysis in order to evaluate differences in expression profiles between two conditions",
"Evaluate the differential alternative splicing in specific genes"
],
- "pageviews": 2082298,
+ "pageviews": 2105145,
"pub_date": "2023-05-17",
"questions": [
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@@ -788045,41 +731749,41 @@
],
"short_id": "T00345",
"short_tools": [
- "cpat",
- "tp_awk_tool",
- "tp_cat",
- "Add_a_column1",
+ "isoformswitchanalyzer",
+ "cat1",
"__FILTER_FROM_FILE__",
- "gene2exon1",
+ "Filter1",
+ "Cut1",
"fastp",
- "stringtie",
- "pygenomeTracks",
- "gffcompare",
- "rseqc_junction_saturation",
- "rna_star",
- "addValue",
- "Remove beginning1",
- "gffread",
"multiqc",
- "Filter1",
+ "stringtie_merge",
+ "collection_element_identifiers",
+ "rna_quast",
+ "rseqc_junction_annotation",
"rseqc_geneBody_coverage",
"rseqc_infer_experiment",
+ "Add_a_column1",
+ "tp_cat",
+ "gffread",
+ "pfamscan",
"tp_grep_tool",
- "isoformswitchanalyzer",
- "stringtie_merge",
- "Cut1",
- "rseqc_junction_annotation",
- "tp_uniq_tool",
"__FLATTEN__",
- "rna_quast",
- "cat1",
- "pfamscan",
- "rseqc_inner_distance",
+ "rseqc_junction_saturation",
+ "gene2exon1",
+ "stringtie",
"fastqc",
- "collection_element_identifiers",
- "sort1",
+ "Remove beginning1",
+ "tp_uniq_tool",
+ "gtftobed12",
+ "addValue",
"rseqc_read_distribution",
- "gtftobed12"
+ "gffcompare",
+ "rseqc_inner_distance",
+ "sort1",
+ "cpat",
+ "tp_awk_tool",
+ "pygenomeTracks",
+ "rna_star"
],
"slides": true,
"slides_recordings": false,
@@ -788096,11 +731800,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -788130,6 +731829,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -788185,10 +731888,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -788235,11 +731934,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -788284,6 +731978,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -788336,10 +732034,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -788380,10 +732074,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -788426,6 +732116,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -788478,10 +732172,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -788522,10 +732212,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -788568,6 +732254,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -788620,10 +732310,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -788664,10 +732350,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -788710,6 +732392,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -788762,10 +732448,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -788806,10 +732488,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -788852,6 +732530,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -788904,10 +732586,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -788948,10 +732626,6 @@
"server": "https://usegalaxy.eu",
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{
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@@ -788994,6 +732668,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.eu",
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"server": "https://usegalaxy.eu",
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{
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@@ -789278,6 +732944,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -789420,6 +733082,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -789562,6 +733220,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
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{
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"state": "missing"
@@ -789712,6 +733362,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -789764,10 +733418,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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{
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@@ -789861,6 +733506,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -789913,10 +733562,6 @@
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{
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"state": "missing"
@@ -790008,6 +733648,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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@@ -790177,6 +733812,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -790201,8 +733840,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
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+ "0.1.1",
+ "0.1.0"
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"server": "https://galaxytrakr.org/",
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{
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"server": "https://usegalaxy.cz/",
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"versions": [
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{
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"versions": [
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+ "0.1.1",
+ "0.1.0"
]
},
{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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@@ -790457,7 +734087,163 @@
"version": "9.3+galaxy1"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.1.1",
+ "1.1.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
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+ "version": "9.3+galaxy1"
+ },
+ {
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+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "inexact",
+ "versions": [
+ "1.1.1"
+ ]
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "1.1.1"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
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+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
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+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "9.3+galaxy1"
+ },
+ {
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+ "state": "missing"
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+ {
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+ {
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+ "state": "missing"
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+ {
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+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
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+ "1.1.0",
+ "1.0.0"
+ ]
+ },
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+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
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+ "1.1.0"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "9.3+galaxy1"
},
@@ -790487,7 +734273,7 @@
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},
{
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
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- "state": "missing"
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- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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{
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{
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@@ -790829,6 +734444,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -790926,9 +734541,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
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@@ -790942,11 +734557,6 @@
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{
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"state": "exact",
@@ -790992,6 +734602,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791016,11 +734630,11 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.3.0",
- "1.5",
- "2.0",
"1.4",
+ "1.5",
"1.2.0",
+ "2.0",
+ "1.3.0",
"1.6"
]
},
@@ -791059,10 +734673,6 @@
"server": "http://galaxy.interactomix.com/",
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- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -791098,9 +734708,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -791108,8 +734718,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -791118,19 +734728,14 @@
"state": "exact",
"version": "2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.3.0",
+ "1.4",
"1.5",
"2.0",
- "1.4",
+ "1.3.0",
"1.6",
"1.3.1"
]
@@ -791175,6 +734780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791200,8 +734809,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -791240,10 +734849,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -791269,8 +734874,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -791299,9 +734904,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -791312,11 +734917,6 @@
"state": "exact",
"version": "0.74+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -791365,6 +734965,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791420,10 +735024,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -791457,10 +735057,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -791473,11 +735073,6 @@
"state": "exact",
"version": "2.2.1.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -791523,6 +735118,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791578,10 +735177,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -791615,10 +735210,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -791633,11 +735228,6 @@
"state": "exact",
"version": "2.2.1.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -791687,6 +735277,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791742,10 +735336,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -791779,10 +735369,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
- "2.2.1.1"
+ "2.2.1.1",
+ "0.11.4.1",
+ "2.2.1.0"
]
},
{
@@ -791797,18 +735387,10 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
- "0.11.4.1",
"2.2.1.2",
"2.2.1.1",
- "2.2.1.3+galaxy0",
- "2.2.1.4+galaxy0"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
+ "0.11.4.1",
+ "2.2.1.0",
"2.2.1.3+galaxy0",
"2.2.1.4+galaxy0"
]
@@ -791827,8 +735409,8 @@
"state": "inexact",
"versions": [
"0.11.6.0",
- "2.2.1.0",
"2.2.1.2",
+ "2.2.1.0",
"2.2.1.3+galaxy0",
"2.2.1.4+galaxy0"
]
@@ -791872,6 +735454,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -791926,10 +735512,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -791974,11 +735556,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -792024,6 +735601,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792088,10 +735669,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -792129,11 +735706,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -792148,11 +735725,6 @@
"state": "exact",
"version": "0.23.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -792205,6 +735777,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792260,10 +735836,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -792297,9 +735869,9 @@
"state": "inexact",
"versions": [
"0.11.2",
+ "0.9.8+galaxy1",
"0.9.8",
- "0.10.6",
- "0.9.8+galaxy1"
+ "0.10.6"
]
},
{
@@ -792312,11 +735884,6 @@
"state": "exact",
"version": "0.12.6+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.12.6+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -792364,6 +735931,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792417,10 +735988,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -792465,11 +736032,6 @@
"state": "exact",
"version": "357"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "357"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -792515,6 +736077,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792567,10 +736133,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -792613,11 +736175,6 @@
"state": "exact",
"version": "1.20.0+galaxy5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.20.0+galaxy5"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -792662,6 +736219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792716,10 +736277,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -792768,11 +736325,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -792783,8 +736335,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -792827,6 +736379,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -792882,10 +736438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -792918,14 +736470,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.6",
- "3.3",
+ "3.2.1",
"2.0.1",
- "2.0.0",
+ "3.1.1.1",
"3.1.2",
+ "3.6",
"3.1.1",
- "3.2.1",
- "3.1.1.1"
+ "3.3",
+ "2.0.0"
]
},
{
@@ -792940,11 +736492,6 @@
"state": "exact",
"version": "3.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -792994,6 +736541,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -793047,10 +736598,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -793083,14 +736630,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.6",
- "3.3",
+ "3.2.1",
"2.0.1",
- "2.0.0",
+ "3.1.1.1",
"3.1.2",
+ "3.6",
"3.1.1",
- "3.2.1",
- "3.1.1.1"
+ "3.3",
+ "2.0.0"
]
},
{
@@ -793103,11 +736650,6 @@
"state": "exact",
"version": "3.8+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.8+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -793157,6 +736699,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -793216,10 +736762,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -793261,8 +736803,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -793270,11 +736812,6 @@
"state": "exact",
"version": "2.7.11a+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.11a+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -793327,6 +736864,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -793352,8 +736893,8 @@
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -793388,10 +736929,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -793430,24 +736967,24 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -793455,11 +736992,6 @@
"state": "exact",
"version": "2.7.11a+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.11a+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -793512,6 +737044,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -793564,10 +737100,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -793613,11 +737145,6 @@
"state": "exact",
"version": "2.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -793668,6 +737195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -793720,10 +737251,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -793769,11 +737296,6 @@
"state": "exact",
"version": "2.2.3+galaxy0"
},
- {
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@@ -793818,6 +737340,10 @@
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"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -793913,10 +737435,10 @@
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- "1.3.3",
+ "1.0.0",
"2.1.1",
"1.3.4",
- "1.0.0"
+ "1.3.3"
]
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@@ -793931,11 +737453,6 @@
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@@ -793985,6 +737502,10 @@
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+ "state": "missing"
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{
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"server": "https://mississippi.sorbonne-universite.fr",
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@@ -794080,9 +737597,9 @@
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+ "2.1.1",
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+ "1.3.4"
]
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+ "2.1.7",
+ "2.1.7+galaxy1"
]
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@@ -794151,6 +737663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -794204,10 +737720,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -794241,8 +737753,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.4galaxy2",
- "2.6.4.3"
+ "2.6.4.3",
+ "2.4galaxy2"
]
},
{
@@ -794258,11 +737770,6 @@
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},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -794313,6 +737820,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -794366,10 +737877,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -794420,11 +737927,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -794474,6 +737976,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -794527,10 +738033,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -794581,11 +738083,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -794635,6 +738132,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -794688,10 +738189,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -794742,11 +738239,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -794796,6 +738288,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -794849,10 +738345,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -794886,8 +738378,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.6.4.1",
- "2.4galaxy1"
+ "2.4galaxy1",
+ "2.6.4.1"
]
},
{
@@ -794903,11 +738395,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -794957,6 +738444,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -795010,10 +738501,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -795064,11 +738551,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -795169,7 +738651,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 272,
- "visitors": 879749,
+ "visitors": 889337,
"workflows": [
{
"creators": [
@@ -795501,7 +738983,7 @@
],
"license": "MIT",
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-->|output| 12;\n 13[\"gather fastp reports\"];\n 8 -->|report_json| 13;\n 14[\"RNA STAR\"];\n 1 -->|output| 14;\n 2 -->|output| 14;\n 8 -->|output_paired_coll| 14;\n 15[\"Gene BED To Exon/Intron/Codon BED\"];\n 9 -->|bed_file| 15;\n 16[\"gffread\"];\n 10 -->|output| 16;\n 2 -->|output| 16;\n 17[\"gffread\"];\n 11 -->|output| 17;\n 2 -->|output| 17;\n 18[\"gather FastQC reports\"];\n 12 -->|text_file| 18;\n 19[\"Concatenate datasets\"];\n 14 -->|splice_junctions| 19;\n 20[\"Compute\"];\n 15 -->|out_file1| 20;\n 21[\"Filter\"];\n 19 -->|out_file1| 21;\n 22[\"Sort\"];\n 20 -->|out_file1| 22;\n 23[\"Cut\"];\n 21 -->|out_file1| 23;\n 24[\"Text reformatting\"];\n 22 -->|out_file1| 24;\n 25[\"Text reformatting\"];\n 22 -->|out_file1| 25;\n 26[\"Sort\"];\n 23 -->|out_file1| 26;\n 27[\"Unique lines\"];\n 26 -->|out_file1| 27;\n 28[\"RNA STAR\"];\n 1 -->|output| 28;\n 2 -->|output| 28;\n 8 -->|output_paired_coll| 28;\n 27 -->|outfile| 28;\n 29[\"StringTie\"];\n 1 -->|output| 29;\n 28 -->|mapped_reads| 29;\n 30[\"Infer Experiment\"];\n 28 -->|mapped_reads| 30;\n 9 -->|bed_file| 30;\n 31[\"Gene Body Coverage BAM\"];\n 28 -->|mapped_reads| 31;\n 9 -->|bed_file| 31;\n 32[\"Junction Saturation\"];\n 28 -->|mapped_reads| 32;\n 9 -->|bed_file| 32;\n 33[\"Junction Annotation\"];\n 28 -->|mapped_reads| 33;\n 9 -->|bed_file| 33;\n 34[\"Inner Distance\"];\n 28 -->|mapped_reads| 34;\n 9 -->|bed_file| 34;\n 35[\"Read Distribution\"];\n 28 -->|mapped_reads| 35;\n 9 -->|bed_file| 35;\n 36[\"StringTie merge\"];\n 1 -->|output| 36;\n 29 -->|output_gtf| 36;\n 37[\"gffread\"];\n 29 -->|output_gtf| 37;\n 2 -->|output| 37;\n 38[\"MultiQC\"];\n 28 -->|output_log| 38;\n 28 -->|reads_per_gene| 38;\n 30 -->|output| 38;\n 32 -->|outputr| 38;\n 31 -->|outputtxt| 38;\n 34 -->|outputfreqtxt| 38;\n 35 -->|output| 38;\n 33 -->|stats| 38;\n 39[\"StringTie\"];\n 36 -->|out_gtf| 39;\n 28 -->|mapped_reads| 39;\n 40[\"GffCompare\"];\n 1 -->|output| 40;\n 36 -->|out_gtf| 40;\n 41[\"Plot a transcript in intron\"];\n 28 -->|signal_unique_str2| 41;\n 28 -->|signal_unique_str1| 41;\n 36 -->|out_gtf| 41;\n 42[\"gffread\"];\n 36 -->|out_gtf| 42;\n 2 -->|output| 42;\n 43[\"Plot ADD3\"];\n 28 -->|signal_unique_str2| 43;\n 28 -->|signal_unique_str1| 43;\n 36 -->|out_gtf| 43;\n 44[\"Plot ADD3 zoomed\"];\n 28 -->|signal_unique_str2| 44;\n 28 -->|signal_unique_str1| 44;\n 36 -->|out_gtf| 44;\n 45[\"rnaQUAST\"];\n 1 -->|output| 45;\n 2 -->|output| 45;\n 37 -->|output_exons| 45;\n 46[\"Extract element identifiers\"];\n 39 -->|transcript_expression| 46;\n 47[\"Filter\"];\n 40 -->|tmap_output| 47;\n 48[\"Search in textfiles\"];\n 46 -->|output| 48;\n 49[\"Filter collection\"];\n 48 -->|output| 49;\n 39 -->|transcript_expression| 49;\n 50[\"IsoformSwitchAnalyzeR\"];\n 1 -->|output| 50;\n 49 -->|output_discarded| 50;\n 36 -->|out_gtf| 50;\n 49 -->|output_filtered| 50;\n 42 -->|output_exons| 50;\n 51[\"IsoformSwitchAnalyzeR\"];\n 50 -->|switchList| 51;\n 52[\"PfamScan\"];\n 5 -->|output| 52;\n 51 -->|isoformAA| 52;\n 4 -->|output| 52;\n 3 -->|output| 52;\n 53[\"CPAT\"];\n 16 -->|output_exons| 53;\n 51 -->|isoformNT| 53;\n 17 -->|output_exons| 53;\n 2 -->|output| 53;\n 54[\"Cut\"];\n 53 -->|orf_seqs_prob_best| 54;\n 55[\"Add column\"];\n 54 -->|out_file1| 55;\n 56[\"Remove beginning\"];\n 55 -->|out_file1| 56;\n 57[\"Concatenate datasets\"];\n 6 -->|output| 57;\n 56 -->|out_file1| 57;\n 58[\"IsoformSwitchAnalyzeR\"];\n 57 -->|out_file1| 58;\n 52 -->|output| 58;\n 51 -->|switchList| 58;\n 59[\"IsoformSwitchAnalyzeR\"];\n 57 -->|out_file1| 59;\n 52 -->|output| 59;\n 51 -->|switchList| 59;\n d2f0865b-20ba-43ef-8ebc-ad9f517ec60d[\"Output\\nconsequencesSummary\"];\n 59 --> d2f0865b-20ba-43ef-8ebc-ad9f517ec60d;\n style d2f0865b-20ba-43ef-8ebc-ad9f517ec60d stroke:#2c3143,stroke-width:4px;\n 8dd90968-6ef6-48e1-a104-547cbeaa80c8[\"Output\\nconsequencesEnrichment\"];\n 59 --> 8dd90968-6ef6-48e1-a104-547cbeaa80c8;\n style 8dd90968-6ef6-48e1-a104-547cbeaa80c8 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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "GTN_differential_isoform_expression",
"outputs": [
{
@@ -795750,23 +739232,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n owner: bgruening\n revisions: 53e9709776a0\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n owner: bgruening\n revisions: 1bfc7254232e\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_manipulation\n owner: devteam\n revisions: bb07615a5b6a\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3fdc1a74d866\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtool_filter2\n owner: devteam\n revisions: dc6ff68ea5e8\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n owner: iuc\n revisions: c78cf6fe3018\n tool_panel_section_label: BED\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n owner: iuc\n revisions: 24a09ca67621\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n owner: iuc\n revisions: 1eb21dccc2fa\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json",
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- "authorship": [
- "malloryfreeberg"
- ],
- "reviewing": [
- "shiltemann",
- "nsoranzo",
- "bebatut",
- "bgruening",
- "lecorguille",
- "malloryfreeberg",
- "willdurand",
- "mvdbeek",
- "njall",
- "hexylena"
- ]
- },
"contributors": [
{
"id": "malloryfreeberg",
@@ -795775,198 +739240,21 @@
"orcid": "0000-0003-2949-3921",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
- },
- {
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- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "elixir-europe"
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- "joined": "2017-09",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
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- "lon": 3.08
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- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
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],
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"RNA-Seq analysis",
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- "Gene expression analysis",
- "Sequence alignment",
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+ "Sequence alignment",
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],
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@@ -796000,7 +739288,7 @@
"Differentiate between subclasses of small RNAs based on their characteristics.",
"Identify differently abundant small RNAs and their targets."
],
- "pageviews": 11269,
+ "pageviews": 11281,
"pub_date": "2017-06-29",
"questions": [
"What small RNAs are expressed?",
@@ -796008,15 +739296,15 @@
],
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"deseq2",
- "samtool_filter2",
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"hisat2",
"trim_galore",
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- "bedtools_bamtofastq"
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{
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"url": "https://usegalaxy.no/",
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"1.9.0+galaxy2",
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]
},
@@ -796544,6 +739811,10 @@
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@@ -796710,6 +739969,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -796762,10 +740025,6 @@
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@@ -796875,6 +740125,10 @@
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@@ -796900,8 +740154,8 @@
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- "0.74+galaxy1"
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@@ -797026,8 +740265,8 @@
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"0.72",
+ "0.73+galaxy0",
"0.74+galaxy0",
"0.69",
"0.71",
@@ -797065,6 +740304,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -797120,10 +740363,6 @@
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@@ -797172,14 +740411,6 @@
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{
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"state": "inexact",
@@ -797230,6 +740461,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -797254,8 +740489,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
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- "2.27.0.0"
+ "2.27.0.0",
+ "2.27.1"
]
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{
@@ -797286,10 +740521,6 @@
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{
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@@ -797336,10 +740567,6 @@
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{
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@@ -797356,8 +740583,8 @@
"server": "https://usegalaxy.org.au",
"state": "inexact",
"versions": [
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- "2.27.0.0"
+ "2.27.0.0",
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]
},
{
@@ -797390,6 +740617,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -797414,9 +740645,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
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"2.11.40.6",
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@@ -797507,26 +740734,13 @@
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+ "2.11.40.7+galaxy0",
+ "2.11.40.6+galaxy2"
]
},
{
@@ -797569,6 +740783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -797630,10 +740848,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -797683,17 +740897,6 @@
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- "2.2.1+galaxy0"
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{
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"state": "inexact",
@@ -797701,8 +740904,8 @@
"2.1.0+galaxy5",
"2.1.0+galaxy7",
"2.2.1+galaxy1",
- "2.1.0+galaxy6",
- "2.2.1+galaxy0"
+ "2.2.1+galaxy0",
+ "2.1.0+galaxy6"
]
},
{
@@ -797718,9 +740921,9 @@
"2.1.0+galaxy4",
"2.1.0+galaxy7",
"2.2.1+galaxy1",
+ "2.2.1+galaxy0",
"2.1.0+galaxy6",
- "2.1.0",
- "2.2.1+galaxy0"
+ "2.1.0"
]
},
{
@@ -797766,7 +740969,7 @@
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"video_view": 0,
"visit_duration": 129,
- "visitors": 6191,
+ "visitors": 6201,
"workflows": [
{
"creators": [],
@@ -797894,7 +741097,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nrRNA reference FASTA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nmiRNA hairpin reference FASTA\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"FastQC\"];\n 0 -->|output| 3;\n 4[\"Trim Galore!\"];\n 0 -->|output| 4;\n 5[\"FastQC\"];\n 4 -->|trimmed_reads_single| 5;\n 6[\"HISAT\"];\n 4 -->|trimmed_reads_single| 6;\n 1 -->|output| 6;\n 7[\"Filter SAM or BAM, output SAM or BAM\"];\n 6 -->|output_alignments| 7;\n 8[\"Convert from BAM to FastQ\"];\n 7 -->|output1| 8;\n 9[\"HISAT\"];\n 8 -->|output| 9;\n 2 -->|output| 9;\n 10[\"Filter SAM or BAM, output SAM or BAM\"];\n 9 -->|output_alignments| 10;\n 11[\"Convert from BAM to FastQ\"];\n 10 -->|output1| 11;\n 12[\"Manipulate FASTQ\"];\n 11 -->|output| 12;\n 13[\"Manipulate FASTQ\"];\n 11 -->|output| 13;\n 14[\"FastQC\"];\n 12 -->|output_file| 14;\n 15[\"FastQC\"];\n 13 -->|output_file| 15;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)",
"outputs": [
{
@@ -798516,7 +741719,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Salmon\"];\n 1 -->|output| 4;\n 0 -->|output| 4;\n 5[\"Salmon\"];\n 1 -->|output| 5;\n 0 -->|output| 5;\n 6[\"Salmon\"];\n 1 -->|output| 6;\n 2 -->|output| 6;\n 7[\"Salmon\"];\n 1 -->|output| 7;\n 2 -->|output| 7;\n 8[\"DESeq2\"];\n 6 -->|output_quant| 8;\n 4 -->|output_quant| 8;\n 3 -->|output| 8;\n 9[\"DESeq2\"];\n 7 -->|output_quant| 9;\n 5 -->|output_quant| 9;\n 3 -->|output| 9;\n 10[\"Filter\"];\n 8 -->|deseq_out| 10;\n 11[\"Filter\"];\n 9 -->|deseq_out| 11;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "sRNA Seq Step 2: Salmon And DESeq2",
"outputs": [],
"parent_id": "transcriptomics/srna",
@@ -798598,17 +741801,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n owner: devteam\n revisions: 02026300aa45\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: egsea\n owner: iuc\n revisions: fba1660fb717\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fgsea\n owner: iuc\n revisions: 17eb1e0d711f\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goseq\n owner: iuc\n revisions: ef2ad746b589\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "bphipson"
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- "reviewing": [
- "bgruening",
- "nsoranzo",
- "hexylena"
- ]
- },
"contributors": [
{
"id": "mblue9",
@@ -798624,91 +741816,13 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
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+ "Gene set testing",
"Gene-set enrichment analysis",
- "Gene set testing"
+ "Gene functional annotation"
],
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"exact_supported_servers": [
@@ -798741,20 +741855,20 @@
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],
- "pageviews": 38092,
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],
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- "fgsea",
- "Add_a_column1",
"tp_sort_header_tool",
+ "Cut1",
"goseq",
+ "fgsea",
+ "Add_a_column1",
"join1",
- "Cut1",
+ "tp_cut_tool",
"egsea"
],
"slides": false,
@@ -798818,6 +741932,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -798873,10 +741991,6 @@
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"url": "http://galaxy.interactomix.com/"
},
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -798923,11 +742037,6 @@
"url": "https://usegalaxy.eu",
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},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -798972,6 +742081,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -799024,10 +742137,6 @@
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{
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"state": "local"
@@ -799068,10 +742177,6 @@
"server": "https://usegalaxy.eu",
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},
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- "state": "local"
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{
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"state": "local"
@@ -799114,6 +742219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -799166,10 +742275,6 @@
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{
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@@ -799210,10 +742315,6 @@
"server": "https://usegalaxy.eu",
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{
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"state": "local"
@@ -799256,6 +742357,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -799310,10 +742415,6 @@
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{
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@@ -799361,11 +742462,6 @@
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{
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"state": "exact",
@@ -799411,6 +742507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -799515,11 +742611,6 @@
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{
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"state": "exact",
@@ -799565,6 +742656,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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"state": "missing"
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{
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@@ -799661,9 +742752,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -799671,8 +742762,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.0",
"1.4",
+ "2.0",
"1.1.0"
]
},
@@ -799681,11 +742772,6 @@
"state": "exact",
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{
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"state": "exact",
@@ -799731,6 +742817,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -799783,10 +742873,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -799819,8 +742905,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
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- "1.6.0.1"
+ "1.6.0.1",
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]
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"state": "exact",
@@ -799882,6 +742964,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -799934,10 +743020,6 @@
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@@ -799981,11 +743063,6 @@
"state": "exact",
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},
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- "state": "exact",
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{
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"state": "exact",
@@ -800031,6 +743108,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -800086,10 +743167,6 @@
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{
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"state": "inexact",
@@ -800125,14 +743202,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.2.2",
+ "1.34.0+galaxy1",
+ "1.30.1",
"1.30.0",
+ "0.2.2",
"1.26.0",
- "1.36.0+galaxy0",
- "1.30.1",
- "1.34.0",
"1.32.0",
- "1.34.0+galaxy1"
+ "1.34.0",
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]
},
{
@@ -800147,11 +743224,6 @@
"state": "exact",
"version": "1.44.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.44.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -800212,7 +743284,7 @@
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"video_view": 0,
"visit_duration": 114,
- "visitors": 23065,
+ "visitors": 23131,
"workflows": [
{
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@@ -800425,7 +743497,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "RNA Seq Genes To Pathways (imported from uploaded file)",
"outputs": [
{
@@ -801159,19 +744231,6 @@
},
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- "xiliu"
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- "reviewing": [
- "shiltemann",
- "bgruening",
- "lecorguille"
- ]
- },
"contributors": [
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@@ -801226,94 +744285,19 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/xiliu/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/xiliu.json"
- },
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- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
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- "lat": 47.997791,
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- "matrix": "bgruening:matrix.org",
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- "twitter": "bjoerngruening",
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- },
- {
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- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/transcriptomics/tutorials/full-de-novo",
"draft": true,
"edam_operation": [
- "Statistical calculation",
- "Sequencing quality control",
- "De-novo assembly",
"Validation",
"de Novo sequencing",
+ "De-novo assembly",
+ "Transcriptome assembly",
+ "Statistical calculation",
+ "Sequencing quality control",
"Sequence composition calculation",
"Coding region prediction",
- "Transcriptome assembly",
"Gene functional annotation"
],
"edam_topic": [],
@@ -801347,7 +744331,7 @@
"They are single sentences describing what a learner should be able to do once they have completed the tutorial",
"You can use Bloom's Taxonomy to write effective learning objectives"
],
- "pageviews": 22934,
+ "pageviews": 22994,
"pub_date": "2020-02-13",
"questions": [
"Which biological questions are addressed by the tutorial?",
@@ -801355,21 +744339,21 @@
],
"short_id": "T00290",
"short_tools": [
+ "trinity_run_de_analysis",
+ "trinity_filter_low_expr_transcripts",
+ "trinity_align_and_estimate_abundance",
+ "trinity_define_clusters_by_cutting_tree",
+ "trinotate",
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- "describe_samples",
"trinity_samples_qccheck",
+ "describe_samples",
+ "trimmomatic",
+ "trinity_contig_exn50_statistic",
"trinity_abundance_estimates_to_matrix",
- "trinotate",
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- "trinity_run_de_analysis",
- "trinity_align_and_estimate_abundance",
- "trinity_define_clusters_by_cutting_tree",
- "trinity_analyze_diff_expr"
+ "transdecoder"
],
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"slides_recordings": false,
@@ -801426,6 +744410,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -801531,11 +744515,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -801580,6 +744559,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"state": "inexact",
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -801670,8 +744649,8 @@
"versions": [
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{
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"state": "inexact",
@@ -801762,6 +744730,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -801814,16 +744786,12 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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"versions": [
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- "2.15.1+galaxy0"
+ "2.15.1+galaxy0",
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{
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"state": "exact",
@@ -801918,6 +744877,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -801943,9 +744906,9 @@
"state": "inexact",
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+ "1.6",
"1.11+galaxy0",
- "1.7",
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]
},
{
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{
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
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+ ]
+ },
+ {
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{
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+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
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"versions": [
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]
},
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+ "state": "inexact",
+ "versions": [
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+ "1.7.1"
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+ "1.3.1",
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+ "servers": [
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+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
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+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
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+ "state": "missing"
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+ "state": "missing"
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+ ]
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+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
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+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
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+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
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+ "state": "missing"
+ },
{
"server": "https://neo.engr.uconn.edu/",
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@@ -802015,100 +745160,49 @@
},
{
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- "state": "inexact",
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- ]
+ "state": "missing"
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{
"server": "https://usegalaxy.be/",
- "state": "inexact",
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+ "state": "exact",
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{
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- "state": "exact",
- "version": "1.2.0"
+ "state": "inexact",
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+ ]
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{
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"state": "exact",
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- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy1",
- "1.24.1+galaxy0"
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+ "version": "3.0.1"
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{
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- "1.8+galaxy0",
- "1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
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+ "state": "exact",
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- "1.24.1+galaxy0",
- "1.5.0",
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+ "state": "exact",
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+ "state": "exact",
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}
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4",
"servers": [
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@@ -802130,6 +745224,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -802152,7 +745250,8 @@
},
{
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+ "state": "exact",
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{
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@@ -802162,7 +745261,8 @@
"server": "https://galaxytrakr.org/",
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"versions": [
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+ "2.9.1+galaxy1",
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]
},
{
@@ -802185,13 +745285,14 @@
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
+ "state": "inexact",
+ "versions": [
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+ "2.15.1+galaxy0",
+ "2.15.1+galaxy1"
+ ]
},
{
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@@ -802220,49 +745321,55 @@
{
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+ "version": "2.8.4"
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{
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"state": "inexact",
"versions": [
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+ "2.9.1+galaxy2",
+ "2.15.1+galaxy1"
]
},
{
"server": "https://usegalaxy.eu",
"state": "exact",
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- "server": "https://usegalaxy.fr/",
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+ "version": "2.8.4"
},
{
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- "state": "exact",
- "version": "3.0.1"
+ "state": "inexact",
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+ "2.9.1+galaxy2",
+ "2.15.1+galaxy1"
+ ]
},
{
"server": "https://usegalaxy.org",
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+ "state": "inexact",
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+ "2.9.1+galaxy2",
+ "2.15.1+galaxy0",
+ "2.15.1+galaxy1",
+ "2.8.5"
+ ]
},
{
"server": "https://usegalaxy.org.au",
"state": "exact",
- "version": "3.0.1"
+ "version": "2.8.4"
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{
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"state": "missing"
}
],
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4",
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@@ -802284,6 +745391,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
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@@ -802306,8 +745417,7 @@
},
{
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- "version": "2.8.4"
+ "state": "missing"
},
{
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- "versions": [
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- "2.9.1+galaxy1"
- ]
+ "state": "missing"
},
{
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"server": "http://galaxy.interactomix.com/",
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- "2.15.1+galaxy1",
+ "2.9.1",
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+ "2.9.1"
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- "2.9.1+galaxy1",
- "2.15.1+galaxy1",
+ "2.9.1",
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4",
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@@ -802463,6 +745547,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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+ "2.15.1+galaxy0",
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- },
{
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"state": "inexact",
"versions": [
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"2.9.1"
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"2.15.1+galaxy0",
+ "2.9.1+galaxy1",
+ "2.9.1",
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@@ -803955,10 +746810,10 @@
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@@ -804132,8 +746972,8 @@
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- "visitors": 11981,
+ "visit_duration": 149,
+ "visitors": 12032,
"workflows": [
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@@ -804256,7 +747096,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 20[\"Trinotate\"];\n 18 -->|transdecoder_pep| 20;\n 21[\"Differential expression analysis\"];\n 19 -->|TPM_no_norm_gene| 21;\n 3 -->|output| 21;\n 22[\"Extract and cluster differentially expressed transcripts\"];\n 21 -->|DE_results| 22;\n 19 -->|norm_TMM| 22;\n 3 -->|output| 22;\n 23[\"Partition genes into expression clusters\"];\n 22 -->|rdata| 23;\n 1[\"\u2139\ufe0f Input Collection\\nCollection of R2 reads\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 0[\"\u2139\ufe0f Input Collection\\nCollection of R1 reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nSamples description\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 2[\"Describe samples\"];\n 5[\"FastQC\"];\n 1 -->|output| 5;\n 4[\"FastQC\"];\n 0 -->|output| 4;\n 7[\"MultiQC\"];\n 5 -->|text_file| 7;\n 4 -->|text_file| 7;\n 6[\"Trimmomatic\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 9[\"FastQC\"];\n 6 -->|fastq_out_r2_paired| 9;\n 8[\"FastQC\"];\n 6 -->|fastq_out_r1_paired| 8;\n 11[\"MultiQC\"];\n 9 -->|text_file| 11;\n 8 -->|text_file| 11;\n 10[\"Trinity\"];\n 6 -->|fastq_out_r2_paired| 10;\n 6 -->|fastq_out_r1_paired| 10;\n 13[\"Build expression matrix\"];\n 12 -->|genes_counts_rsem| 13;\n 12[\"Align reads and estimate abundance\"];\n 10 -->|assembled_transcripts| 12;\n 6 -->|fastq_out_r2_paired| 12;\n 6 -->|fastq_out_r1_paired| 12;\n 15[\"Filter low expression transcripts\"];\n 10 -->|assembled_transcripts| 15;\n 13 -->|TPM_no_norm_gene| 15;\n 14[\"RNASeq samples quality check\"];\n 13 -->|trans_counts| 14;\n 3 -->|output| 14;\n 17[\"Align reads and estimate abundance\"];\n 15 -->|filtered| 17;\n 6 -->|fastq_out_r1_paired| 17;\n 6 -->|fastq_out_r2_paired| 17;\n 16[\"Compute contig Ex90N50 statistic and Ex90 transcript count\"];\n 10 -->|assembled_transcripts| 16;\n 13 -->|trans_counts| 16;\n 19[\"Build expression matrix\"];\n 17 -->|genes_counts_rsem| 19;\n 18[\"TransDecoder\"];\n 15 -->|filtered| 18;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "trinity NG",
"outputs": [
{
@@ -804920,18 +747760,6 @@
},
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- "bgruening",
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- "hexylena",
- "shiltemann"
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"contributors": [
{
"id": "mblue9",
@@ -804940,128 +747768,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
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- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
}
],
"dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot",
@@ -805072,7 +747778,6 @@
"MISSISSIPPI",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -805108,7 +747813,7 @@
"objectives": [
"Create a volcano plot of RNA-seq data to visualize significant genes"
],
- "pageviews": 233286,
+ "pageviews": 233710,
"pub_date": "2018-12-31",
"questions": [
"How to generate a volcano plot from RNA-seq data?"
@@ -805178,11 +747883,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -805234,6 +747934,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -805289,10 +747993,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -805339,11 +748039,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -805388,6 +748083,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -805445,10 +748144,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -805483,8 +748178,8 @@
"state": "inexact",
"versions": [
"0.0.3",
- "0.0.2",
- "0.0.1"
+ "0.0.1",
+ "0.0.2"
]
},
{
@@ -805497,11 +748192,6 @@
"state": "exact",
"version": "0.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -805552,7 +748242,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 81,
- "visitors": 137821,
+ "visitors": 138181,
"workflows": [
{
"creators": [],
@@ -805690,7 +748380,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nDE results\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nVolcano genes\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Volcano plot highlighting significant\"];\n 0 -->|output| 2;\n 3[\"Volcano plot labelling top 10\"];\n 0 -->|output| 3;\n 4[\"Volcano plot labelling genes of interest\"];\n 0 -->|output| 4;\n 1 -->|output| 4;\n 16aef53e-11fd-4def-a7fb-6cf9a98f0902[\"Output\\nvolcano_pdf\"];\n 4 --> 16aef53e-11fd-4def-a7fb-6cf9a98f0902;\n style 16aef53e-11fd-4def-a7fb-6cf9a98f0902 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Visualization Of RNA-Seq Results With Volcano Plot",
"outputs": [
{
@@ -805895,24 +748585,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_multi_bam_summary\n owner: bgruening\n revisions: 004aea905d4d\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_correlation\n owner: bgruening\n revisions: fd408d755394\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_fingerprint\n owner: bgruening\n revisions: 793665fff0f8\n tool_panel_section_label: deepTools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bctools_extract_alignment_ends\n owner: iuc\n revisions: 6d41997eabdc\n tool_panel_section_label: Transcriptomics\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n owner: iuc\n revisions: b8348686a0b9\n tool_panel_section_label: BED\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n owner: iuc\n revisions: a1a923cd89e8\n tool_panel_section_label: BED\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: extract_genomic_dna\n owner: iuc\n revisions: 5cc8e93ee98f\n tool_panel_section_label: Fetch Sequences/Alignments\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meme_chip\n owner: iuc\n revisions: cc100e0f61f4\n tool_panel_section_label: Motif Tools\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n owner: iuc\n revisions: 980d2a2e1180\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_dedup\n owner: iuc\n revisions: f1d33e4c7bd8\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n owner: iuc\n revisions: f3759eec3018\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 135b80fb1ac2\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peakachu\n owner: rnateam\n revisions: 886f5adba83d\n tool_panel_section_label: Peak Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rcas\n owner: rnateam\n revisions: 7c7a2a381dfe\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/clipseq/tutorial.json",
- "contributions": {
- "authorship": [
- "heylf",
- "dmaticzka",
- "bebatut"
- ],
- "reviewing": [
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- "bgruening",
- "shiltemann",
- "hexylena",
- "nsoranzo",
- "bebatut",
- "heylf",
- "lecorguille",
- "njall"
- ]
- },
"contributors": [
{
"elixir_node": "de",
@@ -805962,204 +748634,17 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
"twitter": "bebatut",
"url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
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- "elixir_node": "ch",
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- "joined": "2019-08",
- "location": {
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- "lat": 46.52,
- "lon": 6.56
- },
- "name": "Lucille Delisle",
- "orcid": "0000-0002-1964-4960",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
- },
- {
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
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- "elixir-europe"
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- "contact_for_training": true,
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- "twitter": "NicolaSoranzo",
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- "contact_for_training": true,
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- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
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- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- "former_affiliations": [
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- "id": "heylf",
- "joined": "2018-08",
- "name": "Florian Heyl",
- "orcid": "0000-0002-3651-5685",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/heylf/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/heylf.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/transcriptomics/tutorials/clipseq",
"edam_operation": [
+ "Read pre-processing",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
- "Sequence alignment",
- "Primer removal",
"Sequence composition calculation",
+ "Primer removal",
"Mapping",
+ "Sequence alignment",
"Sequence trimming"
],
"edam_topic": [],
@@ -806194,7 +748679,7 @@
"Analyse the peaks and find potential binding motifs and targets",
"Check the quality of the peak calling"
],
- "pageviews": 15048,
+ "pageviews": 15069,
"pub_date": "2018-08-17",
"questions": [
"How is raw CLIP-Seq data processed and analysed?",
@@ -806202,26 +748687,26 @@
],
"short_id": "T00288",
"short_tools": [
- "tp_awk_tool",
- "meme_chip",
+ "Extract genomic DNA 1",
"deeptools_plot_correlation",
- "rna_star",
+ "cutadapt",
+ "rcas",
"__MERGE_COLLECTION__",
"bctools_extract_alignment_ends",
+ "wig_to_bigWig",
+ "fastqc",
"bedtools_genomecoveragebed_bedgraph",
- "deeptools_multi_bam_summary",
"umi_tools_dedup",
- "deeptools_plot_fingerprint",
"bedtools_slopbed",
- "wig_to_bigWig",
- "rcas",
+ "peakachu",
+ "deeptools_plot_fingerprint",
"__SORTLIST__",
- "fastqc",
- "cutadapt",
+ "meme_chip",
"sort1",
- "umi_tools_extract",
- "peakachu",
- "Extract genomic DNA 1"
+ "tp_awk_tool",
+ "rna_star",
+ "deeptools_multi_bam_summary",
+ "umi_tools_extract"
],
"slides": false,
"slides_recordings": false,
@@ -806262,6 +748747,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -806317,10 +748806,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -806367,11 +748852,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -806416,6 +748896,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -806468,10 +748952,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -806512,10 +748992,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -806558,6 +749034,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -806610,10 +749090,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -806654,10 +749130,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -806700,6 +749172,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -806752,10 +749228,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -806796,10 +749268,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -806842,6 +749310,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -806896,10 +749368,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -806935,10 +749403,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.2.0",
"2.5.1.1.0",
+ "2.5.7.0",
"3.3.2.0.0",
- "2.5.7.0"
+ "3.0.2.0"
]
},
{
@@ -806954,11 +749422,6 @@
"state": "exact",
"version": "3.5.1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.5.1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807004,6 +749467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -807060,10 +749527,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -807100,9 +749563,9 @@
"state": "inexact",
"versions": [
"3.3.2.0.0",
- "2.5.1.1.0",
"3.0.2.0",
- "2.5.7.0"
+ "2.5.7.0",
+ "2.5.1.1.0"
]
},
{
@@ -807118,11 +749581,6 @@
"state": "exact",
"version": "3.5.1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.5.1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807168,6 +749626,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -807224,10 +749686,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -807264,9 +749722,9 @@
"state": "inexact",
"versions": [
"3.3.2.0.0",
+ "2.5.1.1.0",
"2.5.7.0",
- "3.0.2.0",
- "2.5.1.1.0"
+ "3.0.2.0"
]
},
{
@@ -807282,11 +749740,6 @@
"state": "exact",
"version": "3.5.1.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.5.1.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807332,6 +749785,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -807386,10 +749843,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -807436,11 +749889,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807486,6 +749934,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -807543,10 +749995,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -807572,8 +750020,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -807597,12 +750045,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -807612,9 +750060,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -807625,11 +750073,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807676,149 +750119,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
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- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "0.2.2"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "0.2.2"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.2.2"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.2.2"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "missing"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
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- "version": "0.2.2"
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- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
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- {
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- "state": "missing"
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- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -807874,7 +750175,145 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "0.2.2"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "0.2.2"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.2.2"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "0.2.2"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "missing"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.2.2"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -807920,10 +750359,6 @@
"state": "exact",
"version": "2.19.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -807967,6 +750402,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -807991,8 +750430,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "2.27.1",
- "2.27.0.0"
+ "2.27.0.0",
+ "2.27.1"
]
},
{
@@ -808003,8 +750442,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.30.0",
- "2.29.2"
+ "2.29.2",
+ "2.30.0"
]
},
{
@@ -808027,10 +750466,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -808064,14 +750499,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.27.1",
"2.27.0.0",
- "2.30.0",
+ "2.27.1",
"2.29.2",
+ "2.30.0",
"2.31.1+galaxy0",
+ "2.29.0",
"2.19.0",
- "2.24.0",
- "2.29.0"
+ "2.24.0"
]
},
{
@@ -808084,17 +750519,12 @@
"state": "exact",
"version": "2.30.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.30.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.30.0",
"2.29.2",
+ "2.30.0",
"2.19.0"
]
},
@@ -808138,6 +750568,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808191,10 +750625,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -808239,10 +750669,6 @@
"state": "exact",
"version": "3.0.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -808287,6 +750713,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808340,10 +750770,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -808387,10 +750813,6 @@
"state": "exact",
"version": "4.11.2+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -808435,6 +750857,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808460,8 +750886,8 @@
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -808498,10 +750924,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -808538,24 +750960,24 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -808563,11 +750985,6 @@
"state": "exact",
"version": "2.7.8a+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.8a+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -808620,6 +751037,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808675,10 +751096,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -808725,11 +751142,6 @@
"state": "exact",
"version": "1.1.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -808775,6 +751187,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808827,10 +751243,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -808877,11 +751289,6 @@
"state": "exact",
"version": "1.1.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -808927,6 +751334,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -808966,8 +751377,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -808990,10 +751401,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -809036,8 +751443,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -809052,11 +751459,6 @@
"state": "exact",
"version": "4.0+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.0+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -809104,6 +751506,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -809156,10 +751562,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -809205,10 +751607,6 @@
"state": "exact",
"version": "0.1.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -809252,6 +751650,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -809304,10 +751706,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -809351,10 +751749,6 @@
"state": "exact",
"version": "1.5.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -809398,6 +751792,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -809450,10 +751848,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -809494,10 +751888,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -809564,7 +751954,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 116,
- "visitors": 7261,
+ "visitors": 7279,
"workflows": [
{
"creators": [],
@@ -809742,7 +752132,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nBackground\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nEnriched set as a paired-end reads collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nAnnotation Reference File for RCAS\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nGenome Chromosome Sizes\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC\"];\n 0 -->|output| 4;\n 5[\"Cutadapt\"];\n 0 -->|output| 5;\n 6[\"FastQC\"];\n 1 -->|output| 6;\n 7[\"Cutadapt\"];\n 1 -->|output| 7;\n 8[\"UMI-tools extract\"];\n 5 -->|out_pairs| 8;\n 9[\"UMI-tools extract\"];\n 7 -->|out_pairs| 9;\n 10[\"RNA STAR\"];\n 2 -->|output| 10;\n 8 -->|out_paired_collection| 10;\n 11[\"RNA STAR\"];\n 2 -->|output| 11;\n 9 -->|out_paired_collection| 11;\n 12[\"UMI-tools deduplicate\"];\n 10 -->|mapped_reads| 12;\n 13[\"UMI-tools deduplicate\"];\n 11 -->|mapped_reads| 13;\n 14[\"Extract alignment ends\"];\n 12 -->|output| 14;\n 15[\"FastQC\"];\n 12 -->|output| 15;\n 16[\"PEAKachu\"];\n 12 -->|output| 16;\n 13 -->|output| 16;\n 17[\"Merge collections\"];\n 12 -->|output| 17;\n 13 -->|output| 17;\n 18[\"Extract alignment ends\"];\n 13 -->|output| 18;\n 19[\"FastQC\"];\n 13 -->|output| 19;\n 20[\"Sort\"];\n 14 -->|alignment_ends| 20;\n 21[\"Text reformatting\"];\n 16 -->|peak_tables| 21;\n 22[\"Sort collection\"];\n 17 -->|output| 22;\n 23[\"Sort\"];\n 18 -->|alignment_ends| 23;\n 24[\"Create a BedGraph of genome coverage\"];\n 20 -->|out_file1| 24;\n 25[\"bedtools SlopBed\"];\n 3 -->|output| 25;\n 21 -->|outfile| 25;\n 26[\"plotFingerprint\"];\n 22 -->|output| 26;\n 27[\"multiBamSummary\"];\n 22 -->|output| 27;\n 28[\"Create a BedGraph of genome coverage\"];\n 23 -->|out_file1| 28;\n 29[\"Wig/BedGraph-to-bigWig\"];\n 24 -->|output| 29;\n 30[\"Extract Genomic DNA\"];\n 25 -->|output| 30;\n 31[\"Text reformatting\"];\n 25 -->|output| 31;\n 32[\"plotCorrelation\"];\n 27 -->|outFile| 32;\n 33[\"Wig/BedGraph-to-bigWig\"];\n 28 -->|output| 33;\n 34[\"MEME-ChIP\"];\n 30 -->|output| 34;\n 35[\"RCAS\"];\n 31 -->|outfile| 35;\n 2 -->|output| 35;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 ",
"outputs": [
{
@@ -810644,23 +753034,6 @@
},
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- "contributions": {
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- "bphipson",
- "hdashnow"
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- "reviewing": [
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- "hexylena",
- "mtekman",
- "bgruening",
- "mblue9",
- "nsoranzo",
- "bebatut",
- "lecorguille"
- ]
- },
"contributors": [
{
"id": "mblue9",
@@ -810683,193 +753056,22 @@
"name": "Harriet Dashnow",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/hdashnow/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/hdashnow.json"
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- "elixir-europe"
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- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
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- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
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- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
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- "location": {
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- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "elixir_node": "de",
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- "former_affiliations": [
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
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- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
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- "elixir-europe"
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- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
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- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
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- "twitter": "bebatut",
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- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts",
"edam_operation": [
- "Data handling",
+ "RNA-Seq quantification",
+ "Validation",
+ "Sequence trimming",
+ "Read summarisation",
"Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
+ "Sequence composition calculation",
+ "Data handling",
"Formatting",
- "Read summarisation",
"Primer removal",
"Sequence alignment",
- "Validation",
- "Sequence composition calculation",
- "RNA-Seq quantification",
- "Sequence trimming"
+ "Read pre-processing"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -810892,7 +753094,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -810919,7 +753120,7 @@
"Make use of Galaxy Collections for a tidy analysis",
"Create a Galaxy Workflow that converts RNA-seq reads into counts"
],
- "pageviews": 130260,
+ "pageviews": 130521,
"pub_date": "2018-09-23",
"questions": [
"How to convert RNA-seq reads into counts?",
@@ -810945,17 +753146,17 @@
],
"short_id": "T00301",
"short_tools": [
- "picard_MarkDuplicates",
- "samtools_idxstats",
- "fastqc",
- "collection_column_join",
- "cutadapt",
"rseqc_infer_experiment",
- "multiqc",
"featurecounts",
- "rseqc_geneBody_coverage",
+ "fastqc",
+ "multiqc",
+ "cutadapt",
+ "samtools_idxstats",
+ "picard_MarkDuplicates",
"hisat2",
- "rseqc_read_distribution"
+ "collection_column_join",
+ "rseqc_read_distribution",
+ "rseqc_geneBody_coverage"
],
"slides": false,
"slides_recordings": false,
@@ -810984,11 +753185,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -811028,6 +753224,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -811083,10 +753283,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -811133,11 +753329,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -811182,6 +753373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -811243,187 +753438,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
- "0.74+galaxy0"
- ]
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
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@@ -811445,13 +753459,8 @@
},
{
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- "0.72",
- "0.65",
- "0.71"
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+ "state": "exact",
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{
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@@ -811469,18 +753478,8 @@
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{
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- "0.68",
- "0.52",
- "0.74+galaxy1"
- ]
+ "state": "exact",
+ "version": "0.72"
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{
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@@ -811489,9 +753488,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
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"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -811500,37 +753499,35 @@
{
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+ "version": "0.72"
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{
"server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.73+galaxy0"
+ "state": "inexact",
+ "versions": [
+ "0.72+galaxy1",
+ "0.73+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.org",
"state": "exact",
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+ "version": "0.72"
},
{
"server": "https://usegalaxy.org.au",
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+ "version": "0.72"
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{
"server": "https://viralvariant.anses.fr/",
"state": "missing"
}
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+ "version": "0.72"
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{
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"servers": [
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@@ -811552,6 +753549,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -811575,21 +753576,20 @@
{
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+ "version": "0.73+galaxy0"
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{
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- "2.18.2.2",
- "2.18.2.3"
+ "0.74+galaxy0"
]
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+ "state": "exact",
+ "version": "0.73+galaxy0"
+ },
{
"server": "http://hyperbrowser.uio.no/hb/",
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@@ -811610,15 +753610,11 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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{
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"state": "inexact",
"versions": [
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+ "0.74+galaxy0"
]
},
{
@@ -811635,65 +753631,87 @@
},
{
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+ "state": "inexact",
+ "versions": [
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+ "0.72",
+ "0.71",
+ "0.65"
+ ]
},
{
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+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
},
{
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+ "state": "inexact",
+ "versions": [
+ "0.74+galaxy0"
+ ]
},
{
"server": "https://usegalaxy.be/",
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+ "state": "inexact",
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+ "0.72",
+ "0.69",
+ "0.71",
+ "0.65",
+ "0.68",
+ "0.74+galaxy1",
+ "0.52",
+ "0.67"
+ ]
},
{
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
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- "2.18.2.4"
+ "0.74+galaxy0",
+ "0.69",
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+ "0.67",
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},
{
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- ]
+ "state": "exact",
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{
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{
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+ "version": "0.73+galaxy0"
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{
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
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@@ -811715,6 +753733,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
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@@ -811737,11 +753759,8 @@
},
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- "versions": [
- "2.18.2.1",
- "3.1.1.0"
- ]
+ "state": "exact",
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{
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@@ -811749,8 +753768,12 @@
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{
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+ "state": "inexact",
+ "versions": [
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+ "2.18.2.3",
+ "2.7.1.0"
+ ]
},
{
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@@ -811772,10 +753795,6 @@
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{
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- "2.18.2.2"
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+ "state": "exact",
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{
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- "state": "exact",
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+ "state": "inexact",
+ "versions": [
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+ "2.18.2.4"
+ ]
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{
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{
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@@ -811840,22 +753854,22 @@
{
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{
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+ "version": "2.18.2.1"
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{
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}
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3",
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@@ -811877,6 +753891,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -811901,24 +753919,18 @@
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+ "2.18.2.1",
+ "3.1.1.0"
]
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{
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- "state": "inexact",
- "versions": [
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- ]
+ "state": "missing"
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{
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- "versions": [
- "2.0",
- "2.0.3"
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+ "state": "exact",
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{
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@@ -811940,15 +753952,11 @@
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+ "3.1.1.0"
]
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+ "2.18.2.1",
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]
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{
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+ "server": "https://usegalaxy.cz/",
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- "2.0.3"
- ]
+ "server": "https://usegalaxy.eu",
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+ "version": "2.18.2.3"
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{
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"state": "inexact",
"versions": [
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]
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- "2.0.5",
- "2.0",
- "2.0.3",
- "2.0.1"
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+ "state": "exact",
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{
"server": "https://usegalaxy.org.au",
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{
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"state": "missing"
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+ "id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
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@@ -812055,6 +754048,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
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@@ -812077,20 +754074,25 @@
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+ "state": "inexact",
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+ "2.0.5"
+ ]
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{
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+ "state": "inexact",
+ "versions": [
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+ ]
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{
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"state": "inexact",
"versions": [
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+ "2.0.3",
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"state": "missing"
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{
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+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
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+ ]
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+ "state": "missing"
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+ "state": "missing"
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+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
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+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
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+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
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+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "2.0.2"
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+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "2.0.4"
+ ]
+ },
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+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "2.0.2"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "2.0.4",
+ "2.0.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "inexact",
+ "versions": [
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+ "2.0.5",
+ "2.0.3",
+ "2.0",
+ "2.0.1"
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+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
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+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
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+ "state": "missing"
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+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
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+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
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+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
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+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
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+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
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+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
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+ "state": "missing"
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+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
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+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "2.0.4"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "exact",
+ "version": "2.0.4"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "inexact",
+ "versions": [
+ "2.0.3",
+ "2.0"
+ ]
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -812152,8 +754314,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0",
"2.0.3",
+ "2.0",
"2.0.1",
"2.0.2"
]
@@ -812168,11 +754330,6 @@
"state": "exact",
"version": "2.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -812218,6 +754375,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -812271,10 +754432,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -812319,11 +754476,6 @@
"state": "exact",
"version": "0.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -812369,6 +754521,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -812426,10 +754582,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -812482,28 +754634,13 @@
"state": "exact",
"version": "1.6.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.0.3+galaxy2",
- "1.6.4+galaxy1",
- "2.0.1",
- "2.0.3+galaxy1",
- "2.0.6+galaxy0",
- "2.0.1+galaxy1",
- "2.0.3+galaxy0",
- "1.6.4+galaxy2",
- "2.0.1+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.0.1",
- "2.0.1+galaxy1",
"1.6.4+galaxy2",
+ "2.0.1+galaxy1",
"2.0.1+galaxy2"
]
},
@@ -812514,15 +754651,15 @@
"2.0.3+galaxy2",
"1.6.4+galaxy1",
"2.0.1",
+ "1.6.2",
"1.6.3+galaxy2",
"1.4.6.p5",
- "1.6.2",
"2.0.3+galaxy1",
+ "1.6.4+galaxy2",
"1.6.0.3",
- "1.6.0.2",
"2.0.6+galaxy0",
"2.0.1+galaxy1",
- "1.6.4+galaxy2",
+ "1.6.0.2",
"2.0.1+galaxy2",
"1.6.0.6"
]
@@ -812534,14 +754671,14 @@
"2.0.3+galaxy2",
"1.6.4+galaxy1",
"2.0.1",
- "1.6.3+galaxy2",
"1.6.2",
+ "1.6.3+galaxy2",
"2.0.3+galaxy1",
+ "1.6.4+galaxy2",
"2.0.6+galaxy0",
"2.0.1+galaxy1",
- "2.0.3+galaxy0",
- "1.6.4+galaxy2",
"2.0.1+galaxy2",
+ "2.0.3+galaxy0",
"1.6.0.1"
]
},
@@ -812575,6 +754712,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -812636,10 +754777,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -812680,10 +754817,10 @@
"versions": [
"1.6.4+galaxy1",
"1.6.3",
- "1.6.4",
+ "1.6.2",
"1.6.3+galaxy2",
"1.4.6.p5",
- "1.6.2"
+ "1.6.4"
]
},
{
@@ -812699,11 +754836,6 @@
"state": "exact",
"version": "2.0.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -812749,6 +754881,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -812806,10 +754942,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -812859,17 +754991,6 @@
"state": "exact",
"version": "2.1.0+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "2.1.0+galaxy5",
- "2.1.0+galaxy7",
- "2.2.1+galaxy1",
- "2.1.0+galaxy6",
- "2.2.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -812877,8 +754998,8 @@
"2.1.0+galaxy5",
"2.1.0+galaxy7",
"2.2.1+galaxy1",
- "2.1.0+galaxy6",
- "2.2.1+galaxy0"
+ "2.2.1+galaxy0",
+ "2.1.0+galaxy6"
]
},
{
@@ -812894,9 +755015,9 @@
"2.1.0+galaxy4",
"2.1.0+galaxy7",
"2.2.1+galaxy1",
+ "2.2.1+galaxy0",
"2.1.0+galaxy6",
- "2.1.0",
- "2.2.1+galaxy0"
+ "2.1.0"
]
},
{
@@ -812929,6 +755050,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -812990,10 +755115,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813035,9 +755156,9 @@
"2.1.0+galaxy4",
"2.2.1+galaxy1",
"2.0.5.1",
- "1.0.0",
"2.1.0+galaxy2",
- "2.0.3"
+ "2.0.3",
+ "1.0.0"
]
},
{
@@ -813052,11 +755173,6 @@
"state": "exact",
"version": "2.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.2.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -813102,6 +755218,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -813156,10 +755276,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813212,11 +755328,6 @@
"state": "exact",
"version": "1.11+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -813262,6 +755373,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -813321,10 +755436,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813377,20 +755488,6 @@
"state": "exact",
"version": "1.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "1.11+galaxy1",
- "1.11+galaxy0",
- "1.7",
- "1.9+galaxy1",
- "1.9",
- "1.8+galaxy0",
- "1.8+galaxy1",
- "1.24.1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -813401,8 +755498,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -813445,6 +755542,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -813499,10 +755600,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813555,11 +755652,6 @@
"state": "exact",
"version": "1.7"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -813605,6 +755697,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -813644,8 +755740,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -813668,10 +755764,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813724,31 +755816,6 @@
"state": "exact",
"version": "1.16.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.0+galaxy0",
- "4.8+galaxy1",
- "4.9+galaxy1",
- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
- "3.5+galaxy0",
- "3.4+galaxy2",
- "4.6+galaxy0",
- "3.4+galaxy1",
- "4.6+galaxy1",
- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -813796,6 +755863,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -813835,8 +755906,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -813859,10 +755930,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -813905,8 +755972,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -813921,11 +755988,6 @@
"state": "exact",
"version": "3.7+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.7+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -813973,6 +756035,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -814028,10 +756094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -814081,11 +756143,6 @@
"state": "exact",
"version": "2.6.4.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.6.4.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -814131,6 +756188,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -814186,10 +756247,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -814239,11 +756296,6 @@
"state": "exact",
"version": "2.6.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.6.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -814289,6 +756341,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -814344,10 +756400,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -814397,11 +756449,6 @@
"state": "exact",
"version": "2.6.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.6.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -814475,7 +756522,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 152,
- "visitors": 69439,
+ "visitors": 69616,
"workflows": [
{
"creators": [],
@@ -814597,7 +756644,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nReference genes\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nBAM files\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Infer Experiment\"];\n 1 -->|output| 2;\n 0 -->|output| 2;\n 3[\"MarkDuplicates\"];\n 1 -->|output| 3;\n 4[\"Samtools idxstats\"];\n 1 -->|output| 4;\n 5[\"MultiQC\"];\n 2 -->|output| 5;\n 3 -->|metrics_file| 5;\n 4 -->|output| 5;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "QC report",
"outputs": [
{
@@ -814865,7 +756912,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 10[\"Infer Experiment\"];\n 5 -->|output_alignments| 10;\n 1 -->|output| 10;\n 11[\"Read Distribution\"];\n 5 -->|output_alignments| 11;\n 1 -->|output| 11;\n 12[\"Column Join\"];\n 6 -->|output_short| 12;\n 13[\"MultiQC\"];\n 4 -->|text_file| 13;\n 3 -->|report| 13;\n 10 -->|output| 13;\n 7 -->|metrics_file| 13;\n 8 -->|output| 13;\n 9 -->|outputtxt| 13;\n 11 -->|output| 13;\n 6 -->|output_summary| 13;\n 5 -->|summary_file| 13;\n 2[\"FastQC raw reads\"];\n 0 -->|output| 2;\n 3[\"Cutadapt\"];\n 0 -->|output| 3;\n 4[\"FastQC post QC\"];\n 3 -->|out1| 4;\n 5[\"HISAT2\"];\n 3 -->|out1| 5;\n 6[\"featureCounts\"];\n 5 -->|output_alignments| 6;\n 7[\"MarkDuplicates\"];\n 5 -->|output_alignments| 7;\n 8[\"Samtools idxstats\"];\n 5 -->|output_alignments| 8;\n 9[\"Gene Body Coverage BAM\"];\n 5 -->|output_alignments| 9;\n 1 -->|output| 9;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "RNA Seq Reads To Counts",
"outputs": [],
"parent_id": "transcriptomics/rna-seq-reads-to-counts",
@@ -814941,16 +756988,6 @@
},
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@@ -815073,7 +757036,7 @@
"Look and learn what the shapes of the read profiles represent",
"Clustering of the read profiles by machine learning algorithm"
],
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"questions": [
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@@ -815081,10 +757044,10 @@
],
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"short_tools": [
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"tp_sort_header_tool",
"blockclust",
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"slides_recordings": false,
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},
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{
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"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -815201,10 +757168,6 @@
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{
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"url": "https://mississippi.sorbonne-universite.fr",
@@ -815251,11 +757214,6 @@
"url": "https://usegalaxy.eu",
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -815300,6 +757258,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
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"state": "missing"
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{
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"state": "inexact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -815454,6 +757407,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -815489,8 +757446,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
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- "2.0.3"
+ "2.0.3",
+ "2.0"
]
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@@ -815513,10 +757470,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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@@ -815562,22 +757515,13 @@
"state": "exact",
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{
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"state": "inexact",
"versions": [
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- "2.0.3"
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]
},
{
@@ -815625,6 +757569,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
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"server": "http://galaxy.interactomix.com/",
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{
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{
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"state": "exact",
@@ -815774,6 +757714,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -815826,10 +757770,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -815876,10 +757816,6 @@
"state": "exact",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -815932,8 +757868,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 180,
- "visitors": 904,
+ "visit_duration": 179,
+ "visitors": 907,
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@@ -816011,7 +757947,7 @@
],
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+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Blockclust 1.1.0 Clustering",
"outputs": [
{
@@ -816280,26 +758216,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: 74a8bef53a00\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n owner: devteam\n revisions: f2aac0c5c60d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n owner: iuc\n revisions: 1a125daea0d8\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: limma_voom\n owner: iuc\n revisions: d5a940112511\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "mritchie",
- "hdashnow",
- "Shians",
- "charitylaw"
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- "hexylena",
- "bgruening",
- "nsoranzo",
- "xgaia",
- "mblue9"
- ]
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"contributors": [
{
"id": "mblue9",
@@ -816358,139 +758274,12 @@
"name": "Charity Law",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/charitylaw/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/charitylaw.json"
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- "nfdi4plants",
- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
- "erasmusmc"
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- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lat": 51.912,
- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
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- "avans-atgm",
- "uni-freiburg"
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- "lat": 51.91,
- "lon": 4.46
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- "elixir-europe"
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- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
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- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "id": "xgaia",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/xgaia/",
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- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
}
],
"dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes",
"edam_operation": [
- "Annotation",
- "RNA-Seq analysis"
+ "RNA-Seq analysis",
+ "Annotation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -816515,7 +758304,6 @@
"id": "transcriptomics/rna-seq-counts-to-genes",
"inexact_supported_servers": [
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.org.au"
],
"js_requirements": {
@@ -816536,7 +758324,7 @@
"Visualisation and interactive exploration of count data",
"Identification of differentially expressed genes"
],
- "pageviews": 66858,
+ "pageviews": 66953,
"pub_date": "2018-12-31",
"questions": [
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@@ -816554,11 +758342,11 @@
],
"short_id": "T00298",
"short_tools": [
- "tp_cut_tool",
- "tp_replace_in_line",
"mergeCols1",
+ "limma_voom",
"annotatemyids",
- "limma_voom"
+ "tp_cut_tool",
+ "tp_replace_in_line"
],
"slides": false,
"slides_recordings": false,
@@ -816582,11 +758370,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org.au",
"url": "https://usegalaxy.org.au",
@@ -816616,6 +758399,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -816671,10 +758458,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -816721,11 +758504,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -816770,6 +758548,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -816824,10 +758606,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
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- "version": "1.1.0"
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{
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"state": "exact",
@@ -816925,6 +758698,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -816983,10 +758760,6 @@
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@@ -817036,15 +758809,6 @@
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"state": "exact",
@@ -817090,6 +758854,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
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"state": "missing"
@@ -817142,10 +758910,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -817189,13 +758953,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -817242,6 +758999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -817298,10 +759059,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -817342,8 +759099,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
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- "3.16.0+galaxy1"
+ "3.16.0+galaxy1",
+ "3.17.0+galaxy1"
]
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{
@@ -817351,29 +759108,14 @@
"state": "exact",
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- "state": "inexact",
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{
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"state": "inexact",
"versions": [
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- "3.12.0+galaxy1",
+ "3.7.0+galaxy2",
"3.14.0+galaxy0",
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]
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@@ -817389,12 +759131,12 @@
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"3.7.0+galaxy1",
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"3.16.0+galaxy1",
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- "3.14.0+galaxy0",
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"3.17.0+galaxy0",
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+ "3.7.0+galaxy2",
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]
},
{
@@ -817427,6 +759169,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -817479,10 +759225,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -817528,42 +759270,30 @@
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- "state": "inexact",
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- "3.48.0+galaxy1",
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
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- "3.50.0+galaxy0",
+ "3.48.0",
"3.48.0+galaxy1",
"3.48.0+galaxy2",
- "3.48.0"
+ "3.50.0+galaxy0"
]
},
{
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
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"3.38.3+galaxy3",
- "3.34.9.7",
"3.38.3+galaxy2",
+ "3.34.9.8",
+ "3.34.9.7",
"3.50.1+galaxy0",
- "3.58.1+galaxy0",
+ "3.48.0",
"3.48.0+galaxy1",
"3.48.0+galaxy2",
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+ "3.58.1+galaxy0"
]
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{
@@ -817573,11 +759303,11 @@
"3.38.3+galaxy3",
"3.38.3+galaxy2",
"3.50.1+galaxy0",
- "3.50.0+galaxy0",
- "3.58.1+galaxy0",
+ "3.48.0",
"3.48.0+galaxy1",
"3.48.0+galaxy2",
- "3.48.0"
+ "3.58.1+galaxy0",
+ "3.50.0+galaxy0"
]
},
{
@@ -817624,7 +759354,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 135,
- "visitors": 38338,
+ "visitors": 38416,
"workflows": [
{
"creators": [],
@@ -817715,7 +759445,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nsampleinfo\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Cut\"];\n 0 -->|output| 2;\n 3[\"Merge Columns\"];\n 1 -->|output| 3;\n 4[\"Replace Text\"];\n 2 -->|output| 4;\n 5[\"Cut\"];\n 3 -->|out_file1| 5;\n 6[\"annotateMyIDs\"];\n 4 -->|outfile| 6;\n 7[\"limma\"];\n 4 -->|outfile| 7;\n 6 -->|out_tab| 7;\n 5 -->|output| 7;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "RNA Seq Counts To Genes",
"outputs": [],
"parent_id": "transcriptomics/rna-seq-counts-to-genes",
@@ -817834,23 +759564,6 @@
},
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"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
- "contributions": {
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- "pavanvidem",
- "beatrizserrano"
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- "bgruening",
- "bebatut",
- "beatrizserrano",
- "pavanvidem",
- "gallardoalba",
- "hexylena",
- "natefoo"
- ]
- },
"contributors": [
{
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@@ -817888,188 +759601,21 @@
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"twitter": "BSerranoSolano",
"url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
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- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
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- "gallantries",
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- "linkedin": "shiltemann",
- "location": {
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "joined": "2017-09",
- "linkedin": "bgruening",
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- "matrix": "bgruening:matrix.org",
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- "elixir-europe",
- "elixir-converge"
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- "former_affiliations": [
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- "lon": 4.46
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- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "name": "Nate Coraor",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
- "twitter": "natefoo",
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}
],
"dir": "topics/transcriptomics/tutorials/mirna-target-finder",
"edam_operation": [
- "Statistical calculation",
+ "RNA-Seq quantification",
+ "Validation",
+ "Sequence trimming",
"RNA-Seq analysis",
+ "Statistical calculation",
"Sequencing quality control",
- "Gene expression analysis",
- "Read pre-processing",
+ "Sequence composition calculation",
"Primer removal",
- "Validation",
"Differential gene expression analysis",
- "Sequence composition calculation",
- "RNA-Seq quantification",
- "Sequence trimming"
+ "Gene expression analysis",
+ "Read pre-processing"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -818101,7 +759647,7 @@
"Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
"Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
],
- "pageviews": 5673182,
+ "pageviews": 5696026,
"pub_date": "2021-04-08",
"questions": [
"Which miRNAs are upregulated in response to brassinosteroids?",
@@ -818123,20 +759669,20 @@
],
"short_id": "T00292",
"short_tools": [
+ "cat1",
+ "Filter1",
+ "Cut1",
"deseq2",
- "fastqc",
- "filter_by_fasta_ids",
+ "sample_seqs",
"rbc_mirdeep2_mapper",
"rbc_mirdeep2_quantifier",
- "__MERGE_COLLECTION__",
- "multiqc",
- "Filter1",
"sort1",
- "sample_seqs",
- "targetfinder",
+ "fastqc",
+ "multiqc",
+ "__MERGE_COLLECTION__",
"salmon",
- "cat1",
- "Cut1",
+ "targetfinder",
+ "filter_by_fasta_ids",
"trim_galore"
],
"slides": true,
@@ -818214,6 +759760,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -818269,10 +759819,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -818319,11 +759865,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -818368,6 +759909,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -818420,10 +759965,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -818464,10 +760005,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -818510,6 +760047,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -818562,10 +760103,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -818606,10 +760143,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
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{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -818652,6 +760185,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -818704,10 +760241,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
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- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -818748,10 +760281,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -818794,6 +760323,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -818846,10 +760379,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- {
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- "state": "local"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -818890,10 +760419,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
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@@ -819736,6 +761225,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -819760,9 +761253,9 @@
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -820085,9 +761568,9 @@
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{
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@@ -820180,11 +761659,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -820230,6 +761704,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -820283,10 +761761,6 @@
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@@ -820329,11 +761803,6 @@
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{
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"state": "exact",
@@ -820379,6 +761848,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -820431,10 +761904,6 @@
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{
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@@ -820480,13 +761949,6 @@
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{
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"state": "inexact",
@@ -820534,6 +761996,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -820586,10 +762052,6 @@
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{
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"state": "missing"
@@ -820632,11 +762094,6 @@
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- "state": "exact",
- "version": "2.0.0"
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{
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"state": "exact",
@@ -820682,6 +762139,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -820734,10 +762195,6 @@
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{
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@@ -820780,10 +762237,6 @@
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- "state": "missing"
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{
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"state": "inexact",
@@ -820855,8 +762308,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 312,
- "visitors": 2097078,
+ "visit_duration": 311,
+ "visitors": 2111677,
"workflows": [
{
"creators": [],
@@ -821157,7 +762610,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n style 7 stroke:#2c3143,stroke-width:4px;\n 8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n style 8 stroke:#2c3143,stroke-width:4px;\n 9[\"FastQC\"];\n 0 -->|output| 9;\n 10[\"Trim Galore!\"];\n 0 -->|output| 10;\n 11[\"FastQC\"];\n 1 -->|output| 11;\n 12[\"Trim Galore!\"];\n 1 -->|output| 12;\n 13[\"FastQC\"];\n 2 -->|output| 13;\n 14[\"FastQC\"];\n 4 -->|output| 14;\n 15[\"Salmon quant\"];\n 6 -->|output| 15;\n 2 -->|output| 15;\n 5 -->|output| 15;\n 16[\"Salmon quant\"];\n 6 -->|output| 16;\n 4 -->|output| 16;\n 5 -->|output| 16;\n 17[\"FastQC\"];\n 10 -->|trimmed_reads_single| 17;\n 18[\"MiRDeep2 Mapper\"];\n 10 -->|trimmed_reads_single| 18;\n 19[\"Merge collections\"];\n 11 -->|text_file| 19;\n 9 -->|text_file| 19;\n 20[\"FastQC\"];\n 12 -->|trimmed_reads_single| 20;\n 21[\"MiRDeep2 Mapper\"];\n 12 -->|trimmed_reads_single| 21;\n 22[\"Merge collections\"];\n 13 -->|text_file| 22;\n 14 -->|text_file| 22;\n 23[\"DESeq2\"];\n 15 -->|output_gene_quant| 23;\n 16 -->|output_gene_quant| 23;\n 6 -->|output| 23;\n 24[\"MiRDeep2 Quantifier\"];\n 7 -->|output| 24;\n 3 -->|output| 24;\n 18 -->|output_reads_collapsed| 24;\n 8 -->|output| 24;\n 25[\"MultiQC\"];\n 19 -->|output| 25;\n 26[\"Merge collections\"];\n 20 -->|text_file| 26;\n 17 -->|text_file| 26;\n 27[\"MiRDeep2 Quantifier\"];\n 7 -->|output| 27;\n 3 -->|output| 27;\n 21 -->|output_reads_collapsed| 27;\n 8 -->|output| 27;\n 28[\"MultiQC\"];\n 22 -->|output| 28;\n 29[\"Filter\"];\n 23 -->|deseq_out| 29;\n 30[\"Cut\"];\n 24 -->|miRNAsExpressed| 30;\n 31[\"MultiQC\"];\n 26 -->|output| 31;\n 32[\"Cut\"];\n 27 -->|miRNAsExpressed| 32;\n 33[\"Filter\"];\n 29 -->|out_file1| 33;\n 34[\"Filter\"];\n 29 -->|out_file1| 34;\n 35[\"DESeq2\"];\n 32 -->|out_file1| 35;\n 30 -->|out_file1| 35;\n 36[\"Cut\"];\n 34 -->|out_file1| 36;\n 37[\"Filter\"];\n 35 -->|deseq_out| 37;\n 38[\"Filter FASTA\"];\n 36 -->|out_file1| 38;\n 5 -->|output| 38;\n 39[\"Filter\"];\n 37 -->|out_file1| 39;\n 40[\"Filter\"];\n 37 -->|out_file1| 40;\n 41[\"Cut\"];\n 40 -->|out_file1| 41;\n 42[\"Filter FASTA\"];\n 41 -->|out_file1| 42;\n 8 -->|output| 42;\n 43[\"Filter FASTA\"];\n 41 -->|out_file1| 43;\n 7 -->|output| 43;\n 44[\"Concatenate datasets\"];\n 43 -->|output| 44;\n 42 -->|output| 44;\n 45[\"TargetFinder\"];\n 38 -->|output| 45;\n 44 -->|out_file1| 45;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Plant bulk RNA-Seq workflow",
"outputs": [
{
@@ -821782,15 +763235,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_collapse\n owner: iuc\n revisions: 2b2bfeda00d0\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_extract\n owner: iuc\n revisions: e7ee3aadf1a5\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_map\n owner: iuc\n revisions: 95ddee768b61\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_merge\n owner: iuc\n revisions: 6492560fe1b4\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_quantify\n owner: iuc\n revisions: 06ac35533793\n tool_panel_section_label: RNA Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n owner: iuc\n revisions: 33d61c89fb8d\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n owner: lparsons\n revisions: 49370cb85f0f\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json",
- "contributions": {
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- "pavanvidem"
- ],
- "reviewing": [
- "shiltemann",
- "bgruening"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -821803,80 +763247,16 @@
"orcid": "0000-0002-5192-126X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- {
- "affiliations": [
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
}
],
"dir": "topics/transcriptomics/tutorials/rna-interactome",
"edam_operation": [
- "Sequence composition calculation",
- "Statistical calculation",
"Sequencing quality control",
- "Read pre-processing",
+ "Sequence composition calculation",
"Sequence trimming",
- "Primer removal"
+ "Primer removal",
+ "Read pre-processing",
+ "Statistical calculation"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -821910,7 +763290,7 @@
"Quantification of the mapped loci",
"Visualization and filtering of results"
],
- "pageviews": 1985,
+ "pageviews": 1990,
"pub_date": "2020-03-23",
"questions": [
"What are the difficulties in mapping chimeric reads from RNA interactome data?",
@@ -821919,14 +763299,14 @@
],
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- "chira_collapse",
- "cutadapt",
- "chira_map",
"chira_quantify",
"query_tabular",
- "chira_extract",
- "chira_merge"
+ "fastqc",
+ "chira_map",
+ "chira_merge",
+ "cutadapt",
+ "chira_collapse",
+ "chira_extract"
],
"slides": false,
"slides_recordings": false,
@@ -821988,6 +763368,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
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+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -822043,10 +763427,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -822093,11 +763473,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -822142,6 +763517,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822199,10 +763578,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -822253,9 +763628,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -822266,11 +763641,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -822316,6 +763686,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822368,10 +763742,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -822417,10 +763787,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -822468,6 +763834,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822520,10 +763890,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -822569,10 +763935,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -822620,6 +763982,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822672,10 +764038,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -822721,10 +764083,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -822772,6 +764130,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822824,10 +764186,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -822873,10 +764231,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -822924,6 +764278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -822976,10 +764334,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -823025,10 +764379,6 @@
"state": "exact",
"version": "1.4.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -823076,6 +764426,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -823134,10 +764488,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -823184,18 +764534,6 @@
"state": "exact",
"version": "3.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.3.1",
- "3.3.0",
- "3.3.2",
- "3.2.0",
- "3.1.1",
- "3.0.1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -823241,6 +764579,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -823280,8 +764622,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -823304,10 +764646,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -823365,47 +764703,22 @@
"4.7+galaxy0",
"4.4+galaxy0",
"1.16.3",
- "1.6",
"1.16.1",
- "3.5+galaxy0",
+ "1.6",
+ "4.0+galaxy1",
"3.4+galaxy2",
- "4.6+galaxy0",
- "1.16",
+ "1.1.a",
+ "3.7+galaxy0",
+ "3.5+galaxy2",
"3.4+galaxy1",
"4.6+galaxy1",
"3.4+galaxy0",
- "3.7+galaxy0",
- "1.1.a",
- "4.8+galaxy0",
+ "1.16",
"4.9+galaxy0",
- "4.0+galaxy1",
"3.5+galaxy1",
- "3.5+galaxy2"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.0+galaxy0",
- "4.8+galaxy1",
- "4.9+galaxy1",
- "1.16.8",
- "4.7+galaxy0",
- "4.4+galaxy0",
"3.5+galaxy0",
- "3.4+galaxy2",
"4.6+galaxy0",
- "3.4+galaxy1",
- "4.6+galaxy1",
- "3.4+galaxy0",
- "3.7+galaxy0",
- "4.8+galaxy0",
- "4.9+galaxy0",
- "4.0+galaxy1",
- "3.5+galaxy1",
- "3.5+galaxy2",
- "1.16.6"
+ "4.8+galaxy0"
]
},
{
@@ -823464,8 +764777,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 176,
- "visitors": 1262,
+ "visit_duration": 175,
+ "visitors": 1267,
"workflows": [
{
"creators": [],
@@ -823687,7 +765000,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nreads_fastq\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nreference1_fasta\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nreference2_fasta\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nannotation_gtf\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\ngenome_fasta\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"FastQC\"];\n 0 -->|output| 5;\n 6[\"Cutadapt\"];\n 0 -->|output| 6;\n 7[\"FastQC\"];\n 6 -->|out1| 7;\n 8[\"ChiRA collapse\"];\n 6 -->|out1| 8;\n 9[\"ChiRA map\"];\n 8 -->|out| 9;\n 1 -->|output| 9;\n 2 -->|output| 9;\n 10[\"ChiRA merge\"];\n 9 -->|mapped_bed| 10;\n 3 -->|output| 10;\n 1 -->|output| 10;\n 2 -->|output| 10;\n 11[\"ChiRA qauntify\"];\n 10 -->|merged_bed| 11;\n 10 -->|segments_bed| 11;\n 12[\"ChiRA extract\"];\n 4 -->|output| 12;\n 3 -->|output| 12;\n 11 -->|loci| 12;\n 1 -->|output| 12;\n 2 -->|output| 12;\n 7182226d-b48a-4ce1-882e-6bb41091a5d4[\"Output\\ninteractions\"];\n 12 --> 7182226d-b48a-4ce1-882e-6bb41091a5d4;\n style 7182226d-b48a-4ce1-882e-6bb41091a5d4 stroke:#2c3143,stroke-width:4px;\n 011f4c89-d15a-4877-9d49-0146773ce781[\"Output\\nchimeric_reads\"];\n 12 --> 011f4c89-d15a-4877-9d49-0146773ce781;\n style 011f4c89-d15a-4877-9d49-0146773ce781 stroke:#2c3143,stroke-width:4px;\n 13[\"Query Tabular\"];\n 12 -->|chimeras| 13;\n f1315db2-11d1-4dee-9014-eafa1fc0f82f[\"Output\\ndb\"];\n 13 --> f1315db2-11d1-4dee-9014-eafa1fc0f82f;\n style f1315db2-11d1-4dee-9014-eafa1fc0f82f stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "RNA-RNA interactome data analysis - chira v1.4.3",
"outputs": [
{
@@ -824505,20 +765818,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: goenrichment\n owner: iuc\n revisions: 2c7c9646ccf0\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goslimmer\n owner: iuc\n revisions: de3e053bd6a5\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json",
- "contributions": {
- "authorship": [
- "igcbioinformatics",
- "mblue9"
- ],
- "reviewing": [
- "shiltemann",
- "mblue9",
- "igcbioinformatics",
- "bgruening",
- "hexylena",
- "lecorguille"
- ]
- },
"contributors": [
{
"id": "igcbioinformatics",
@@ -824534,125 +765833,6 @@
"orcid": "0000-0003-4847-8436",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "id": "mblue9",
- "joined": "2018-09",
- "name": "Maria Doyle",
- "orcid": "0000-0003-4847-8436",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
- },
- {
- "id": "igcbioinformatics",
- "joined": "2018-12",
- "name": "IGC Bioinformatics Unit",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/igcbioinformatics/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/igcbioinformatics.json"
- },
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- "affiliations": [
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- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
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- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "fr",
- "id": "lecorguille",
- "joined": "2017-09",
- "name": "Gildas Le Corguill\u00e9",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
}
],
"dir": "topics/transcriptomics/tutorials/goenrichment",
@@ -824664,7 +765844,6 @@
"UseGalaxy.be",
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)",
"UseGalaxy.org.au"
@@ -824690,15 +765869,15 @@
"How to perform a GO Enrichment Analysis",
"How to interpret and simplify the results"
],
- "pageviews": 35199,
+ "pageviews": 35243,
"pub_date": "2019-01-23",
"questions": [
"How can I functionally interpret a list of genes of interest that I obtained from my experiment?"
],
"short_id": "T00291",
"short_tools": [
- "goenrichment",
"goslimmer",
+ "goenrichment",
"Filter1"
],
"slides": false,
@@ -824720,11 +765899,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -824765,6 +765939,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -824820,10 +765998,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -824870,11 +766044,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -824919,6 +766088,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -824971,10 +766144,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -825015,10 +766184,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -825061,6 +766226,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -825113,10 +766282,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -825160,11 +766325,6 @@
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},
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- "state": "exact",
- "version": "2.0.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -825210,6 +766370,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -825262,10 +766426,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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@@ -825309,11 +766469,6 @@
"state": "exact",
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- "state": "exact",
- "version": "1.0.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -825365,8 +766520,8 @@
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"video_versions": 0,
"video_view": 0,
- "visit_duration": 79,
- "visitors": 21128,
+ "visit_duration": 80,
+ "visitors": 21163,
"workflows": [
{
"creators": [],
@@ -825639,7 +766794,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "GO Enrichment Workflow",
"outputs": [],
"parent_id": "transcriptomics/goenrichment",
@@ -825714,21 +766869,6 @@
},
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- "bebatut",
- "CicoZhang",
- "mblue9",
- "nsoranzo"
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@@ -825737,165 +766877,13 @@
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
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- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
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],
"dir": "topics/transcriptomics/tutorials/network-analysis-with-heinz",
"edam_operation": [
- "Pathway or network analysis",
"RNA-Seq analysis",
- "Differential gene expression analysis"
+ "Differential gene expression analysis",
+ "Pathway or network analysis"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -825929,19 +766917,19 @@
"objectives": [
"Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork."
],
- "pageviews": 6182329,
+ "pageviews": 6205136,
"pub_date": "2018-10-11",
"questions": [
"Which pathways are potentially contributing to dental caries?"
],
"short_id": "T00293",
"short_tools": [
+ "Cut1",
"deseq2",
"heinz",
"heinz_visualization",
- "heinz_bum",
- "Cut1",
- "heinz_scoring"
+ "heinz_scoring",
+ "heinz_bum"
],
"slides": true,
"slides_recordings": false,
@@ -826003,6 +766991,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -826058,10 +767050,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -826108,11 +767096,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
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- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -826157,6 +767140,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -826209,10 +767196,6 @@
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{
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@@ -826253,10 +767236,6 @@
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"state": "local"
@@ -826299,6 +767278,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -826323,9 +767306,9 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
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"2.11.40.6",
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- "2.11.40.8+galaxy0"
+ "2.11.40.4"
]
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"state": "inexact",
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{
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"state": "inexact",
"versions": [
"2.11.40.6+galaxy1",
- "2.11.40.6+galaxy2",
- "2.11.40.7+galaxy0"
+ "2.11.40.7+galaxy0",
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]
},
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"2.11.40.8+galaxy0",
+ "2.11.40.6",
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"2.11.40.7+galaxy2",
"2.11.39",
- "2.11.40.6+galaxy2",
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+ "2.11.40.7+galaxy1",
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]
},
{
@@ -826486,6 +767452,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -826538,10 +767508,6 @@
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"state": "exact",
@@ -826634,6 +767596,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
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@@ -827208,7 +768158,7 @@
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- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -827428,7 +768255,7 @@
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],
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@@ -827436,9 +768263,9 @@
"short_id": "T00303",
"short_tools": [
"ggplot2_heatmap2",
- "join1",
"datamash_transpose",
- "Cut1"
+ "Cut1",
+ "join1"
],
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"slides_recordings": false,
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{
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"url": "https://usegalaxy.no/",
@@ -827506,6 +768328,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
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{
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"url": "https://usegalaxy.no/",
@@ -827660,6 +768477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"state": "local"
@@ -827802,6 +768615,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
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+ "state": "local"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -827854,10 +768671,6 @@
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{
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"state": "local"
@@ -827898,10 +768711,6 @@
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},
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{
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"state": "local"
@@ -827944,6 +768753,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -828003,10 +768816,6 @@
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@@ -828050,11 +768859,6 @@
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{
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"state": "exact",
@@ -828100,6 +768904,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -828155,10 +768963,6 @@
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{
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"state": "missing"
@@ -828207,18 +769011,6 @@
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{
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"state": "inexact",
@@ -828240,8 +769032,8 @@
"3.1.1+galaxy1",
"3.0.1",
"3.1.3+galaxy0",
- "3.2.0+galaxy1",
"3.2.0+galaxy0",
+ "3.2.0+galaxy1",
"3.1.1"
]
},
@@ -828283,7 +769075,7 @@
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"visit_duration": 83,
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@@ -828294,7 +769086,7 @@
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@@ -828387,8 +769179,8 @@
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],
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"name": "Heatmap2 Workflow",
"outputs": [
{
@@ -828436,7 +769228,7 @@
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"output_name": "output1",
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@@ -828478,22 +769270,6 @@
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"api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-analysis-with-askomics-it/tutorial.json",
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- "hexylena",
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"contributors": [
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@@ -828554,132 +769330,6 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/mboudet.json"
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"url": "https://usegalaxy.eu",
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -829801,6 +770057,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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"state": "missing"
@@ -829943,6 +770195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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"url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
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],
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"name": "Coloc-stats",
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},
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{
"name": "CoralSNP",
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"url": "https://usegalaxy.no/",
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"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
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{
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- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "local"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "local"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "local"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "local"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "local"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "local"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "local"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "local"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "local"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "local"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "local"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "local"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "local"
- }
- ],
- "version": "local"
- },
- {
- "id": "Grouping1",
- "servers": [
- {
- "server": "http://apostl.moffitt.org/",
- "state": "local"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "local"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
@@ -833198,7 +772968,7 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -833220,10 +772990,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -833264,10 +773030,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -833282,17 +773044,17 @@
},
{
"server": "https://viralvariant.anses.fr/",
- "state": "missing"
+ "state": "local"
}
],
"version": "local"
},
{
- "id": "__EXTRACT_DATASET__",
+ "id": "Filter1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://smile.hku.hk/SARGs",
@@ -833308,19 +773070,23 @@
},
{
"server": "https://hyperbrowser.uio.no/coloc-stats",
- "state": "missing"
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
},
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://dintor.eurac.edu/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://www.freebioinfo.org/",
@@ -833336,7 +773102,7 @@
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "missing"
+ "state": "local"
},
{
"server": "https://galaxytrakr.org/",
@@ -833344,11 +773110,11 @@
},
{
"server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://gigagalaxy.net/",
- "state": "missing"
+ "state": "local"
},
{
"server": "https://galaxy-web.ipk-gatersleben.de",
@@ -833360,10 +773126,6 @@
},
{
"server": "http://galaxy.interactomix.com/",
- "state": "local"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
"state": "missing"
},
{
@@ -833380,7 +773142,7 @@
},
{
"server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
+ "state": "local"
},
{
"server": "https://palfinder.ls.manchester.ac.uk/",
@@ -833407,7 +773169,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "Grouping1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "local"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -833430,7 +773326,7 @@
"version": "local"
},
{
- "id": "__FILTER_FROM_FILE__",
+ "id": "__EXTRACT_DATASET__",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -833453,12 +773349,16 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://dintor.eurac.edu/",
@@ -833504,10 +773404,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -833548,10 +773444,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -833572,7 +773464,7 @@
"version": "local"
},
{
- "id": "__FLATTEN__",
+ "id": "__FILTER_FROM_FILE__",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -833594,6 +773486,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -833646,10 +773542,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -833690,10 +773582,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -833714,7 +773602,7 @@
"version": "local"
},
{
- "id": "__MERGE_COLLECTION__",
+ "id": "__FLATTEN__",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -833736,6 +773624,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -833788,10 +773680,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -833832,10 +773720,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -833856,7 +773740,7 @@
"version": "local"
},
{
- "id": "__TAG_FROM_FILE__",
+ "id": "__MERGE_COLLECTION__",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -833878,13 +773762,17 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://dintor.eurac.edu/",
@@ -833930,10 +773818,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -833974,10 +773858,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -833998,11 +773878,11 @@
"version": "local"
},
{
- "id": "cat1",
+ "id": "__TAG_FROM_FILE__",
"servers": [
{
"server": "http://apostl.moffitt.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://smile.hku.hk/SARGs",
@@ -834018,19 +773898,23 @@
},
{
"server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "local"
},
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://dintor.eurac.edu/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://www.freebioinfo.org/",
@@ -834046,19 +773930,19 @@
},
{
"server": "https://galaxy.pasteur.fr/",
- "state": "local"
+ "state": "missing"
},
{
"server": "https://galaxytrakr.org/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://gigagalaxy.net/",
- "state": "local"
+ "state": "missing"
},
{
"server": "https://galaxy-web.ipk-gatersleben.de",
@@ -834070,10 +773954,6 @@
},
{
"server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
"state": "local"
},
{
@@ -834090,7 +773970,7 @@
},
{
"server": "http://galaxy.inf.ethz.ch",
- "state": "local"
+ "state": "missing"
},
{
"server": "https://palfinder.ls.manchester.ac.uk/",
@@ -834116,10 +773996,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -834134,13 +774010,13 @@
},
{
"server": "https://viralvariant.anses.fr/",
- "state": "local"
+ "state": "missing"
}
],
"version": "local"
},
{
- "id": "join1",
+ "id": "cat1",
"servers": [
{
"server": "http://apostl.moffitt.org/",
@@ -834162,6 +774038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -834172,7 +774052,7 @@
},
{
"server": "http://dintor.eurac.edu/",
- "state": "missing"
+ "state": "local"
},
{
"server": "http://www.freebioinfo.org/",
@@ -834192,7 +774072,7 @@
},
{
"server": "https://galaxytrakr.org/",
- "state": "local"
+ "state": "missing"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -834214,10 +774094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -834259,7 +774135,141 @@
"state": "local"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "local"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "local"
+ }
+ ],
+ "version": "local"
+ },
+ {
+ "id": "join1",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "local"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "local"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "local"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "local"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "local"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "local"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "local"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "local"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "local"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "local"
},
{
@@ -834304,6 +774314,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -834328,8 +774342,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -834340,8 +774354,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -834364,10 +774378,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -834408,8 +774418,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -834417,17 +774427,12 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -834470,6 +774475,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -834528,10 +774537,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -834583,11 +774588,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -834636,6 +774636,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -834694,10 +774698,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -834733,8 +774733,8 @@
"versions": [
"1.1.2",
"1.1.0",
- "1.0.0",
- "1.1.1"
+ "1.1.1",
+ "1.0.0"
]
},
{
@@ -834750,11 +774750,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -834804,6 +774799,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -834858,10 +774857,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -834908,11 +774903,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -834958,6 +774948,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835016,10 +775010,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -835071,11 +775061,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -835124,6 +775109,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835178,10 +775167,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -835228,11 +775213,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -835278,6 +775258,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835336,10 +775320,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -835389,11 +775369,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -835441,6 +775416,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835501,10 +775480,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -835538,9 +775513,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -835554,11 +775529,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -835604,6 +775574,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835661,10 +775635,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -835690,8 +775660,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -835715,12 +775685,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -835730,9 +775700,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -835743,11 +775713,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -835793,6 +775758,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -835818,8 +775787,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -835856,10 +775825,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -835883,8 +775848,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -835904,12 +775869,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -835922,11 +775887,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -835975,6 +775935,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836011,9 +775975,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.7.1.0",
"2.18.2.2",
- "2.18.2.3"
+ "2.18.2.3",
+ "2.7.1.0"
]
},
{
@@ -836036,10 +776000,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -836089,11 +776049,6 @@
"state": "exact",
"version": "2.18.2.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -836141,6 +776096,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836174,9 +776133,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.7.1.0",
"2.18.2.2",
- "2.18.2.3"
+ "2.18.2.3",
+ "2.7.1.0"
]
},
{
@@ -836199,10 +776158,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -836253,11 +776208,6 @@
"state": "exact",
"version": "3.1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -836305,6 +776255,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836339,8 +776293,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.0",
- "2.0.3"
+ "2.0.3",
+ "2.0"
]
},
{
@@ -836363,10 +776317,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -836402,8 +776352,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0",
"2.0.3",
+ "2.0",
"2.0.1",
"2.0.2"
]
@@ -836418,11 +776368,6 @@
"state": "exact",
"version": "2.0.4"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.4"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -836468,6 +776413,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836504,8 +776453,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "2.0",
- "2.0.3"
+ "2.0.3",
+ "2.0"
]
},
{
@@ -836528,10 +776477,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -836565,8 +776510,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0",
"2.0.3",
+ "2.0",
"2.0.1",
"2.0.2"
]
@@ -836583,11 +776528,6 @@
"state": "exact",
"version": "2.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -836636,6 +776576,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836690,10 +776634,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -836738,11 +776678,6 @@
"state": "exact",
"version": "0.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -836788,6 +776723,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836842,10 +776781,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -836889,11 +776824,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -836939,6 +776869,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -836996,10 +776930,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -837040,9 +776970,9 @@
"2.11.40.4",
"2.11.40.6+galaxy1",
"2.1.8.0",
+ "2.11.40.2",
"2.11.39",
"2.11.40.3",
- "2.11.40.2",
"2.11.40.5"
]
},
@@ -837056,18 +776986,13 @@
"state": "exact",
"version": "2.11.40.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.11.40.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.11.40.6+galaxy1",
- "2.11.40.6+galaxy2",
- "2.11.40.7+galaxy0"
+ "2.11.40.7+galaxy0",
+ "2.11.40.6+galaxy2"
]
},
{
@@ -837110,6 +777035,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837162,10 +777091,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -837211,11 +777136,6 @@
"state": "exact",
"version": "1.28.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -837261,6 +777181,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837313,10 +777237,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -837362,11 +777282,6 @@
"state": "exact",
"version": "1.28.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.28.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -837412,6 +777327,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837473,10 +777392,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -837517,10 +777432,10 @@
"versions": [
"1.6.4+galaxy1",
"1.6.3",
- "1.6.4",
+ "1.6.2",
"1.6.3+galaxy2",
"1.4.6.p5",
- "1.6.2"
+ "1.6.4"
]
},
{
@@ -837533,18 +777448,13 @@
"state": "exact",
"version": "2.0.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.0.1",
- "2.0.1+galaxy1",
"1.6.4+galaxy2",
+ "2.0.1+galaxy1",
"2.0.1+galaxy2"
]
},
@@ -837588,6 +777498,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837645,10 +777559,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -837687,10 +777597,10 @@
"versions": [
"1.6.4+galaxy1",
"1.6.3",
- "1.6.4",
+ "1.6.2",
"1.6.3+galaxy2",
"1.4.6.p5",
- "1.6.2"
+ "1.6.4"
]
},
{
@@ -837703,18 +777613,13 @@
"state": "exact",
"version": "2.0.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.0.1",
- "2.0.1+galaxy1",
"1.6.4+galaxy2",
+ "2.0.1+galaxy1",
"2.0.1+galaxy2"
]
},
@@ -837758,6 +777663,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837811,10 +777720,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -837850,9 +777755,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.0.1",
"2.2.1",
- "2.2.1+galaxy1"
+ "2.2.1+galaxy1",
+ "3.0.1"
]
},
{
@@ -837867,11 +777772,6 @@
"state": "exact",
"version": "3.1.3.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.1.3.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -837920,6 +777820,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -837973,10 +777877,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -838010,14 +777910,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.2.2",
+ "1.34.0+galaxy1",
+ "1.30.1",
"1.30.0",
+ "0.2.2",
"1.26.0",
- "1.36.0+galaxy0",
- "1.30.1",
- "1.34.0",
"1.32.0",
- "1.34.0+galaxy1"
+ "1.34.0",
+ "1.36.0+galaxy0"
]
},
{
@@ -838030,11 +777930,6 @@
"state": "exact",
"version": "1.50.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.50.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -838080,6 +777975,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838133,10 +778032,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -838181,11 +778076,6 @@
"state": "exact",
"version": "357"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "357"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -838231,6 +778121,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838284,10 +778178,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -838321,8 +778211,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.1.0",
- "0.1.1"
+ "0.1.1",
+ "0.1.0"
]
},
{
@@ -838335,11 +778225,6 @@
"state": "exact",
"version": "0.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -838385,6 +778270,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838439,10 +778328,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -838491,11 +778376,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -838506,8 +778386,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -838550,6 +778430,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838606,10 +778490,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -838655,11 +778535,6 @@
"state": "exact",
"version": "1.34.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.34.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -838705,6 +778580,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838760,10 +778639,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -838796,14 +778671,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.6",
- "3.3",
+ "3.2.1",
"2.0.1",
- "2.0.0",
+ "3.1.1.1",
"3.1.2",
+ "3.6",
"3.1.1",
- "3.2.1",
- "3.1.1.1"
+ "3.3",
+ "2.0.0"
]
},
{
@@ -838818,11 +778693,6 @@
"state": "exact",
"version": "3.8+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.8+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -838872,6 +778742,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -838925,10 +778799,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -838961,14 +778831,14 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "3.6",
- "3.3",
+ "3.2.1",
"2.0.1",
- "2.0.0",
+ "3.1.1.1",
"3.1.2",
+ "3.6",
"3.1.1",
- "3.2.1",
- "3.1.1.1"
+ "3.3",
+ "2.0.0"
]
},
{
@@ -838981,11 +778851,6 @@
"state": "exact",
"version": "3.8+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.8+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -839035,6 +778900,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839060,8 +778929,8 @@
"state": "inexact",
"versions": [
"2.7.8a+galaxy0",
- "2.7.2b",
- "2.7.11a+galaxy0"
+ "2.7.11a+galaxy0",
+ "2.7.2b"
]
},
{
@@ -839098,10 +778967,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -839140,16 +779005,16 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.7.2b",
"2.7.11a+galaxy0",
+ "2.7.2b",
"2.7.8a",
- "2.6.0b-2",
+ "2.5.2b-2",
"2.7.5b",
- "2.7.2a",
- "2.5.2b-0",
"2.7.7a",
- "2.5.2b-2",
- "2.6.0b-1"
+ "2.6.0b-1",
+ "2.5.2b-0",
+ "2.7.2a",
+ "2.6.0b-2"
]
},
{
@@ -839162,11 +779027,6 @@
"state": "exact",
"version": "2.7.10b+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.10b+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -839219,6 +779079,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839278,10 +779142,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -839323,8 +779183,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "2.7.10b+galaxy3",
- "2.7.10b+galaxy4"
+ "2.7.10b+galaxy4",
+ "2.7.10b+galaxy3"
]
},
{
@@ -839332,11 +779192,6 @@
"state": "exact",
"version": "2.7.11a+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.11a+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -839389,6 +779244,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839413,8 +779272,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -839448,10 +779307,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -839501,11 +779356,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -839551,6 +779401,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839607,10 +779461,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -839660,11 +779510,6 @@
"state": "exact",
"version": "1.15.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -839672,9 +779517,9 @@
"1.9+galaxy3",
"1.9+galaxy1",
"1.15.1+galaxy0",
- "1.13+galaxy2",
- "1.13+galaxy1",
"1.9+galaxy2",
+ "1.13+galaxy1",
+ "1.13+galaxy2",
"1.13"
]
},
@@ -839718,6 +779563,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839772,10 +779621,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -839822,11 +779667,6 @@
"state": "exact",
"version": "1.2.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.2.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -839872,6 +779712,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -839909,8 +779753,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.16.9",
- "1.16.8"
+ "1.16.8",
+ "1.16.9"
]
},
{
@@ -839933,10 +779777,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -839979,8 +779819,8 @@
"1.16.8",
"1.16.3",
"1.16.5",
- "1.6",
- "1.16.1"
+ "1.16.1",
+ "1.6"
]
},
{
@@ -839995,11 +779835,6 @@
"state": "exact",
"version": "4.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840047,6 +779882,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840102,10 +779941,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -840141,8 +779976,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.4galaxy2",
- "2.6.4.3"
+ "2.6.4.3",
+ "2.4galaxy2"
]
},
{
@@ -840155,11 +779990,6 @@
"state": "exact",
"version": "5.0.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840210,6 +780040,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840263,10 +780097,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -840300,8 +780130,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.4galaxy2",
- "2.6.4.3"
+ "2.6.4.3",
+ "2.4galaxy2"
]
},
{
@@ -840317,11 +780147,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840372,6 +780197,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840427,10 +780256,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -840480,11 +780305,6 @@
"state": "exact",
"version": "5.0.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840534,6 +780354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840587,10 +780411,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -840641,11 +780461,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840695,6 +780510,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840750,10 +780569,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -840803,11 +780618,6 @@
"state": "exact",
"version": "5.0.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -840857,6 +780667,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -840910,10 +780724,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -840964,11 +780774,6 @@
"state": "exact",
"version": "5.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -841082,7 +780887,7 @@
"video_versions": 2,
"video_view": 0,
"visit_duration": 176,
- "visitors": 150127,
+ "visitors": 150738,
"workflows": [
{
"creators": [
@@ -841427,7 +781232,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nheader\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nKEGG pathways to plot\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Extract samples\u2019 name\"];\n 0 -->|output| 4;\n 5[\"Compute gene length\"];\n 1 -->|output| 5;\n 6[\"Extract groups\"];\n 4 -->|output| 6;\n 7[\"Change Case\"];\n 5 -->|length| 7;\n 8[\"Tag elements with groups\"];\n 0 -->|output| 8;\n 6 -->|outfile| 8;\n 9[\"Differential Analysis\"];\n 8 -->|output| 9;\n c1ff3e9a-46d3-4862-adb6-076ea951be26[\"Output\\nDESeq2_plots\"];\n 9 --> c1ff3e9a-46d3-4862-adb6-076ea951be26;\n style c1ff3e9a-46d3-4862-adb6-076ea951be26 stroke:#2c3143,stroke-width:4px;\n b430e84e-cfa5-48e8-92a7-ef5630ced1e5[\"Output\\nDESeq2_normalized_counts\"];\n 9 --> b430e84e-cfa5-48e8-92a7-ef5630ced1e5;\n style b430e84e-cfa5-48e8-92a7-ef5630ced1e5 stroke:#2c3143,stroke-width:4px;\n 10[\"Compute\"];\n 9 -->|deseq_out| 10;\n 11[\"Annotate DESeq2/DEXSeq output tables\"];\n 1 -->|output| 11;\n 9 -->|deseq_out| 11;\n 12[\"Table Compute\"];\n 9 -->|counts_out| 12;\n 13[\"Cut\"];\n 10 -->|out_file1| 13;\n 14[\"Concatenate datasets\"];\n 2 -->|output| 14;\n 11 -->|output| 14;\n 11f46837-7dbb-453b-962a-3c97cb0faad4[\"Output\\nDESeq2_annotated_results_with_header\"];\n 14 --> 11f46837-7dbb-453b-962a-3c97cb0faad4;\n style 11f46837-7dbb-453b-962a-3c97cb0faad4 stroke:#2c3143,stroke-width:4px;\n 15[\"Table Compute\"];\n 9 -->|counts_out| 15;\n 12 -->|table| 15;\n 32004d23-7c99-4405-a65f-fd861b40c949[\"Output\\nz_score\"];\n 15 --> 32004d23-7c99-4405-a65f-fd861b40c949;\n style 32004d23-7c99-4405-a65f-fd861b40c949 stroke:#2c3143,stroke-width:4px;\n 16[\"Change Case\"];\n 13 -->|out_file1| 16;\n 17[\"Filter\"];\n 14 -->|out_file1| 17;\n 18[\"goseq\"];\n 16 -->|out_file1| 18;\n 7 -->|out_file1| 18;\n a0dd7397-7262-4336-abd6-a915ab6be36a[\"Output\\ngo_genes\"];\n 18 --> a0dd7397-7262-4336-abd6-a915ab6be36a;\n style a0dd7397-7262-4336-abd6-a915ab6be36a stroke:#2c3143,stroke-width:4px;\n 659fec58-4ed5-4aee-9e50-7acce21113cb[\"Output\\ngo_plot\"];\n 18 --> 659fec58-4ed5-4aee-9e50-7acce21113cb;\n style 659fec58-4ed5-4aee-9e50-7acce21113cb stroke:#2c3143,stroke-width:4px;\n c06c58d4-ab5d-49da-b481-baf668c6fc29[\"Output\\ngo_terms\"];\n 18 --> c06c58d4-ab5d-49da-b481-baf668c6fc29;\n style c06c58d4-ab5d-49da-b481-baf668c6fc29 stroke:#2c3143,stroke-width:4px;\n 19[\"goseq\"];\n 16 -->|out_file1| 19;\n 7 -->|out_file1| 19;\n 9872b017-9b39-4cd3-b232-a305979a782b[\"Output\\nkegg_genes\"];\n 19 --> 9872b017-9b39-4cd3-b232-a305979a782b;\n style 9872b017-9b39-4cd3-b232-a305979a782b stroke:#2c3143,stroke-width:4px;\n 8d0ac5be-ac7d-4f10-85ac-d3461f561a50[\"Output\\nkegg_pathways\"];\n 19 --> 8d0ac5be-ac7d-4f10-85ac-d3461f561a50;\n style 8d0ac5be-ac7d-4f10-85ac-d3461f561a50 stroke:#2c3143,stroke-width:4px;\n 20[\"Cut\"];\n 17 -->|out_file1| 20;\n 21[\"Filter\"];\n 17 -->|out_file1| 21;\n 22[\"Filter\"];\n 18 -->|wallenius_tab| 22;\n ae762394-0e90-4b9a-a7b4-7cffeccc80a7[\"Output\\ngo_underrepresented\"];\n 22 --> ae762394-0e90-4b9a-a7b4-7cffeccc80a7;\n style ae762394-0e90-4b9a-a7b4-7cffeccc80a7 stroke:#2c3143,stroke-width:4px;\n 23[\"Filter\"];\n 18 -->|wallenius_tab| 23;\n b788d5b7-119c-418a-a12b-a97ef7ea5bf2[\"Output\\ngo_overrepresented\"];\n 23 --> b788d5b7-119c-418a-a12b-a97ef7ea5bf2;\n style b788d5b7-119c-418a-a12b-a97ef7ea5bf2 stroke:#2c3143,stroke-width:4px;\n 24[\"Filter\"];\n 19 -->|wallenius_tab| 24;\n 69f80c89-fc7d-4bea-836f-34e68615abcd[\"Output\\nkegg_underrepresented\"];\n 24 --> 69f80c89-fc7d-4bea-836f-34e68615abcd;\n style 69f80c89-fc7d-4bea-836f-34e68615abcd stroke:#2c3143,stroke-width:4px;\n 25[\"Filter\"];\n 19 -->|wallenius_tab| 25;\n 930f1461-0ade-4744-a83d-843108c4b597[\"Output\\nkegg_overrepresented\"];\n 25 --> 930f1461-0ade-4744-a83d-843108c4b597;\n style 930f1461-0ade-4744-a83d-843108c4b597 stroke:#2c3143,stroke-width:4px;\n 26[\"Pathview\"];\n 20 -->|out_file1| 26;\n 3 -->|output| 26;\n 7cdd4475-6de3-4c02-be8d-d76e788980f6[\"Output\\npathview_plot\"];\n 26 --> 7cdd4475-6de3-4c02-be8d-d76e788980f6;\n style 7cdd4475-6de3-4c02-be8d-d76e788980f6 stroke:#2c3143,stroke-width:4px;\n 27[\"Join two Datasets\"];\n 9 -->|counts_out| 27;\n 21 -->|out_file1| 27;\n 28[\"Group\"];\n 22 -->|out_file1| 28;\n d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4[\"Output\\ngo_underrepresented_categories\"];\n 28 --> d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4;\n style d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4 stroke:#2c3143,stroke-width:4px;\n 29[\"Group\"];\n 23 -->|out_file1| 29;\n 4d2d01eb-15d2-4863-a522-9462c15eb51c[\"Output\\ngo_overrepresented_categories\"];\n 29 --> 4d2d01eb-15d2-4863-a522-9462c15eb51c;\n style 4d2d01eb-15d2-4863-a522-9462c15eb51c stroke:#2c3143,stroke-width:4px;\n 30[\"Cut\"];\n 27 -->|out_file1| 30;\n 31[\"heatmap2\"];\n 30 -->|out_file1| 31;\n 42cb6b68-4ed6-4b6e-9312-744b9e0c1442[\"Output\\nheatmap_log\"];\n 31 --> 42cb6b68-4ed6-4b6e-9312-744b9e0c1442;\n style 42cb6b68-4ed6-4b6e-9312-744b9e0c1442 stroke:#2c3143,stroke-width:4px;\n 32[\"heatmap2\"];\n 30 -->|out_file1| 32;\n 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3[\"Output\\nheatmap_zscore\"];\n 32 --> 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3;\n style 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "DEG Part - Ref Based RNA Seq - Transcriptomics - GTN",
"outputs": [
{
@@ -842444,7 +782249,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nsingle fastqs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Collection\\npaired fastqs\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Cutadapt: remove bad quality bp\"];\n 0 -->|output| 3;\n 4[\"Flatten paired collection for FastQC\"];\n 1 -->|output| 4;\n 5[\"Cutadapt\"];\n 1 -->|output| 5;\n 6[\"Get gene length\"];\n 2 -->|output| 6;\n 077640cc-edbb-4185-9eb1-d11b522774af[\"Output\\nGene length\"];\n 6 --> 077640cc-edbb-4185-9eb1-d11b522774af;\n style 077640cc-edbb-4185-9eb1-d11b522774af stroke:#2c3143,stroke-width:4px;\n 7[\"convert gtf to bed12\"];\n 2 -->|output| 7;\n 8[\"STAR: map single reads\"];\n 2 -->|output| 8;\n 3 -->|out1| 8;\n 9[\"Merge fastqs for FastQC\"];\n 4 -->|output| 9;\n 0 -->|output| 9;\n 10[\"Merge Cutadapt reports\"];\n 5 -->|report| 10;\n 3 -->|report| 10;\n 11[\"STAR: map paired reads\"];\n 2 -->|output| 11;\n 5 -->|out_pairs| 11;\n 12[\"count reads per gene for SR\"];\n 8 -->|mapped_reads| 12;\n 2 -->|output| 12;\n 13[\"FastQC check read qualities\"];\n 9 -->|output| 13;\n 14[\"Combine cutadapt results\"];\n 10 -->|output| 14;\n cab760db-5c9d-4a3c-b768-998bfbac6b57[\"Output\\nmultiqc_cutadapt_html\"];\n 14 --> cab760db-5c9d-4a3c-b768-998bfbac6b57;\n style cab760db-5c9d-4a3c-b768-998bfbac6b57 stroke:#2c3143,stroke-width:4px;\n 15[\"Merge STAR logs\"];\n 11 -->|output_log| 15;\n 8 -->|output_log| 15;\n 16[\"Merge STAR counts\"];\n 8 -->|reads_per_gene| 16;\n 11 -->|reads_per_gene| 16;\n 17[\"count fragments per gene for PE\"];\n 11 -->|mapped_reads| 17;\n 2 -->|output| 17;\n 1527b5d7-1681-4934-9d9e-3a5f86ae0fee[\"Output\\nfeatureCounts_gene_length\"];\n 17 --> 1527b5d7-1681-4934-9d9e-3a5f86ae0fee;\n style 1527b5d7-1681-4934-9d9e-3a5f86ae0fee stroke:#2c3143,stroke-width:4px;\n 18[\"Merge STAR BAM\"];\n 11 -->|mapped_reads| 18;\n 8 -->|mapped_reads| 18;\n 802017f4-fb1a-4243-b50d-2ed46f746f11[\"Output\\nSTAR_BAM\"];\n 18 --> 802017f4-fb1a-4243-b50d-2ed46f746f11;\n style 802017f4-fb1a-4243-b50d-2ed46f746f11 stroke:#2c3143,stroke-width:4px;\n 19[\"merge coverage unique strand 1\"];\n 8 -->|signal_unique_str1| 19;\n 11 -->|signal_unique_str1| 19;\n 20[\"merge coverage unique strand 2\"];\n 8 -->|signal_unique_str2| 20;\n 11 -->|signal_unique_str2| 20;\n 21[\"Combine FastQC results\"];\n 13 -->|text_file| 21;\n 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd[\"Output\\nmultiqc_fastqc_html\"];\n 21 --> 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd;\n style 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd stroke:#2c3143,stroke-width:4px;\n 22[\"Combine STAR Results\"];\n 15 -->|output| 22;\n 204e3f6c-6f54-46f0-b07c-1f31113265e7[\"Output\\nmultiqc_star_html\"];\n 22 --> 204e3f6c-6f54-46f0-b07c-1f31113265e7;\n style 204e3f6c-6f54-46f0-b07c-1f31113265e7 stroke:#2c3143,stroke-width:4px;\n 23[\"Remove statistics from STAR counts\"];\n 16 -->|output| 23;\n 24[\"Determine library strandness with STAR\"];\n 16 -->|output| 24;\n fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a[\"Output\\nmultiqc_star_counts_html\"];\n 24 --> fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a;\n style fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a stroke:#2c3143,stroke-width:4px;\n 25[\"merge counts from featureCounts\"];\n 12 -->|output_short| 25;\n 17 -->|output_short| 25;\n c82388f8-cb09-4fdf-8a0e-03cdad579f37[\"Output\\nfeatureCounts\"];\n 25 --> c82388f8-cb09-4fdf-8a0e-03cdad579f37;\n style c82388f8-cb09-4fdf-8a0e-03cdad579f37 stroke:#2c3143,stroke-width:4px;\n 26[\"merge featureCounts summary\"];\n 12 -->|output_summary| 26;\n 17 -->|output_summary| 26;\n 27[\"Determine library strandness with Infer Experiment\"];\n 18 -->|output| 27;\n 7 -->|bed_file| 27;\n 940ec3ec-dd2e-4d50-bbc4-756945eb16b2[\"Output\\ninferexperiment\"];\n 27 --> 940ec3ec-dd2e-4d50-bbc4-756945eb16b2;\n style 940ec3ec-dd2e-4d50-bbc4-756945eb16b2 stroke:#2c3143,stroke-width:4px;\n 28[\"Read Distribution\"];\n 18 -->|output| 28;\n 7 -->|bed_file| 28;\n 29[\"Compute read distribution statistics\"];\n 18 -->|output| 29;\n 7 -->|bed_file| 29;\n 30[\"sample BAM\"];\n 18 -->|output| 30;\n 31[\"Get reads number per chromosome\"];\n 18 -->|output| 31;\n 32[\"Remove duplicates\"];\n 18 -->|output| 32;\n 33[\"Determine library strandness with STAR coverage\"];\n 19 -->|output| 33;\n 20 -->|output| 33;\n 2 -->|output| 33;\n 89e1b053-03c2-467a-95a0-d2dc404670ec[\"Output\\npgt\"];\n 33 --> 89e1b053-03c2-467a-95a0-d2dc404670ec;\n style 89e1b053-03c2-467a-95a0-d2dc404670ec stroke:#2c3143,stroke-width:4px;\n 34[\"Select unstranded counts\"];\n 23 -->|outfile| 34;\n bce755be-ac3b-4346-9ac5-1128a287bf00[\"Output\\ncounts_from_star\"];\n 34 --> bce755be-ac3b-4346-9ac5-1128a287bf00;\n style bce755be-ac3b-4346-9ac5-1128a287bf00 stroke:#2c3143,stroke-width:4px;\n 35[\"Sort counts to get gene with highest count on feature Counts\"];\n 25 -->|output| 35;\n 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db[\"Output\\nfeatureCounts_sorted\"];\n 35 --> 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db;\n style 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db stroke:#2c3143,stroke-width:4px;\n 36[\"Combine read asignments statistics\"];\n 26 -->|output| 36;\n fc72242a-f23c-4ceb-9a8b-5280343ea5d6[\"Output\\nmultiqc_featureCounts_html\"];\n 36 --> fc72242a-f23c-4ceb-9a8b-5280343ea5d6;\n style fc72242a-f23c-4ceb-9a8b-5280343ea5d6 stroke:#2c3143,stroke-width:4px;\n 37[\"Combine read distribution on known features\"];\n 29 -->|output| 37;\n 07dca732-0ac7-432e-9e61-2b77f921a23b[\"Output\\nmultiqc_read_distrib\"];\n 37 --> 07dca732-0ac7-432e-9e61-2b77f921a23b;\n style 07dca732-0ac7-432e-9e61-2b77f921a23b stroke:#2c3143,stroke-width:4px;\n 38[\"Get gene body coverage\"];\n 30 -->|outputsam| 38;\n 7 -->|bed_file| 38;\n 39[\"Combine results on reads per chromosome\"];\n 31 -->|output| 39;\n 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf[\"Output\\nmultiqc_reads_per_chrom\"];\n 39 --> 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf;\n style 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf stroke:#2c3143,stroke-width:4px;\n 40[\"Combine results of duplicate reads\"];\n 32 -->|metrics_file| 40;\n 66553d0f-e851-458b-82c2-f9b30e394bac[\"Output\\nmultiqc_dup\"];\n 40 --> 66553d0f-e851-458b-82c2-f9b30e394bac;\n style 66553d0f-e851-458b-82c2-f9b30e394bac stroke:#2c3143,stroke-width:4px;\n 41[\"Sort counts to get gene with highest count on STAR\"];\n 34 -->|out_file1| 41;\n 383df008-0ccb-4d67-98dd-33fa5e2db81e[\"Output\\ncounts_from_star_sorted\"];\n 41 --> 383df008-0ccb-4d67-98dd-33fa5e2db81e;\n style 383df008-0ccb-4d67-98dd-33fa5e2db81e stroke:#2c3143,stroke-width:4px;\n 42[\"Combine gene body coverage\"];\n 38 -->|outputtxt| 42;\n 8544ea5c-faf2-44c9-85d6-40658fc9b9eb[\"Output\\nmultiqc_gene_body_cov\"];\n 42 --> 8544ea5c-faf2-44c9-85d6-40658fc9b9eb;\n style 8544ea5c-faf2-44c9-85d6-40658fc9b9eb stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN",
"outputs": [
{
@@ -843778,7 +783583,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nPaired list collection with PE fastqs\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\ud83d\udee0\ufe0f Subworkflow\\nFastQC\"];\n style 2 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 2;\n 5f7652f1-e225-4ad1-8dbd-4d21544edb89[\"Output\\nmultiqc_fastqc_html\"];\n 2 --> 5f7652f1-e225-4ad1-8dbd-4d21544edb89;\n style 5f7652f1-e225-4ad1-8dbd-4d21544edb89 stroke:#2c3143,stroke-width:4px;\n 3[\"\ud83d\udee0\ufe0f Subworkflow\\ncutadapt\"];\n style 3 fill:#edd,stroke:#900,stroke-width:4px;\n 0 -->|output| 3;\n 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee[\"Output\\nmultiqc_cutadapt_html\"];\n 3 --> 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee;\n style 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee stroke:#2c3143,stroke-width:4px;\n 4[\"\ud83d\udee0\ufe0f Subworkflow\\nSTAR + multiQC\"];\n style 4 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 4;\n 3 -->|out_pairs| 4;\n 8aa5ef30-3f09-4a93-944d-0d89101c056a[\"Output\\nmultiqc_star_html\"];\n 4 --> 8aa5ef30-3f09-4a93-944d-0d89101c056a;\n style 8aa5ef30-3f09-4a93-944d-0d89101c056a stroke:#2c3143,stroke-width:4px;\n 11af5c57-91b4-496c-9b0c-b02904963f81[\"Output\\nSTAR_BAM\"];\n 4 --> 11af5c57-91b4-496c-9b0c-b02904963f81;\n style 11af5c57-91b4-496c-9b0c-b02904963f81 stroke:#2c3143,stroke-width:4px;\n 5[\"\ud83d\udee0\ufe0f Subworkflow\\nmore QC\"];\n style 5 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 5;\n 4 -->|STAR_BAM| 5;\n f2eed352-ca21-4d65-8810-f5a1d3c282b4[\"Output\\nmultiqc_read_distrib_html\"];\n 5 --> f2eed352-ca21-4d65-8810-f5a1d3c282b4;\n style f2eed352-ca21-4d65-8810-f5a1d3c282b4 stroke:#2c3143,stroke-width:4px;\n b306cb12-a275-4c6d-b609-47fdc208864b[\"Output\\nmultiqc_reads_per_chrom_html\"];\n 5 --> b306cb12-a275-4c6d-b609-47fdc208864b;\n style b306cb12-a275-4c6d-b609-47fdc208864b stroke:#2c3143,stroke-width:4px;\n 3375d63c-cdc3-4fbb-8a55-6f504c934918[\"Output\\nmultiqc_gene_body_cov_html\"];\n 5 --> 3375d63c-cdc3-4fbb-8a55-6f504c934918;\n style 3375d63c-cdc3-4fbb-8a55-6f504c934918 stroke:#2c3143,stroke-width:4px;\n 3ea82568-5698-49a7-88fe-91381070aac2[\"Output\\nmultiqc_dup_html\"];\n 5 --> 3ea82568-5698-49a7-88fe-91381070aac2;\n style 3ea82568-5698-49a7-88fe-91381070aac2 stroke:#2c3143,stroke-width:4px;\n 6[\"\ud83d\udee0\ufe0f Subworkflow\\nDetermine strandness\"];\n style 6 fill:#edd,stroke:#900,stroke-width:4px;\n 4 -->|STAR_BAM| 6;\n 1 -->|output| 6;\n 4 -->|signal_unique_str1| 6;\n 4 -->|signal_unique_str2| 6;\n 4 -->|reads_per_gene| 6;\n fb810859-f2d0-43f8-ac7c-5c714c5c6805[\"Output\\ninferexperiment\"];\n 6 --> fb810859-f2d0-43f8-ac7c-5c714c5c6805;\n style fb810859-f2d0-43f8-ac7c-5c714c5c6805 stroke:#2c3143,stroke-width:4px;\n 9727824a-3eb2-4430-92d1-b3c40c3041d1[\"Output\\npgt\"];\n 6 --> 9727824a-3eb2-4430-92d1-b3c40c3041d1;\n style 9727824a-3eb2-4430-92d1-b3c40c3041d1 stroke:#2c3143,stroke-width:4px;\n 105313d8-e31a-405d-8fcd-cc5fd93275e2[\"Output\\nmultiqc_star_counts_html\"];\n 6 --> 105313d8-e31a-405d-8fcd-cc5fd93275e2;\n style 105313d8-e31a-405d-8fcd-cc5fd93275e2 stroke:#2c3143,stroke-width:4px;\n 7[\"\ud83d\udee0\ufe0f Subworkflow\\ncount STAR\"];\n style 7 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 7;\n 4 -->|reads_per_gene| 7;\n 5fee8aff-4023-43f1-a653-f5af5357d798[\"Output\\ncounts_from_star\"];\n 7 --> 5fee8aff-4023-43f1-a653-f5af5357d798;\n style 5fee8aff-4023-43f1-a653-f5af5357d798 stroke:#2c3143,stroke-width:4px;\n bd3388e6-5b45-4fdc-9780-3efd1c34ebf8[\"Output\\ncounts_from_star_sorted\"];\n 7 --> bd3388e6-5b45-4fdc-9780-3efd1c34ebf8;\n style bd3388e6-5b45-4fdc-9780-3efd1c34ebf8 stroke:#2c3143,stroke-width:4px;\n 7b7c698b-4808-4b45-adf1-686f8d273d18[\"Output\\nGene length\"];\n 7 --> 7b7c698b-4808-4b45-adf1-686f8d273d18;\n style 7b7c698b-4808-4b45-adf1-686f8d273d18 stroke:#2c3143,stroke-width:4px;\n 8[\"\ud83d\udee0\ufe0f Subworkflow\\ncount featureCount\"];\n style 8 fill:#edd,stroke:#900,stroke-width:4px;\n 1 -->|output| 8;\n 4 -->|STAR_BAM| 8;\n f0de4714-4df8-4506-90d9-384537ad663e[\"Output\\nfeatureCounts_sorted\"];\n 8 --> f0de4714-4df8-4506-90d9-384537ad663e;\n style f0de4714-4df8-4506-90d9-384537ad663e stroke:#2c3143,stroke-width:4px;\n 8b9d6c76-6e82-4691-b8bc-9996d6ae1594[\"Output\\nfeatureCounts_gene_length\"];\n 8 --> 8b9d6c76-6e82-4691-b8bc-9996d6ae1594;\n style 8b9d6c76-6e82-4691-b8bc-9996d6ae1594 stroke:#2c3143,stroke-width:4px;\n 152ba01e-d4f2-4227-8812-87648a1c19ea[\"Output\\nmultiqc_featureCounts_html\"];\n 8 --> 152ba01e-d4f2-4227-8812-87648a1c19ea;\n style 152ba01e-d4f2-4227-8812-87648a1c19ea stroke:#2c3143,stroke-width:4px;\n 46c7a2e8-7819-4715-a028-7ad1de9ed605[\"Output\\nfeatureCounts\"];\n 8 --> 46c7a2e8-7819-4715-a028-7ad1de9ed605;\n style 46c7a2e8-7819-4715-a028-7ad1de9ed605 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows",
"outputs": [
{
@@ -846812,20 +786617,20 @@
],
"dir": "topics/transcriptomics/tutorials/minerva-pathways",
"edam_operation": [
- "Data handling",
- "Statistical calculation",
- "Sequencing quality control",
+ "RNA-Seq quantification",
+ "Validation",
+ "Annotation",
+ "Read pre-processing",
"RNA-Seq analysis",
"Read summarisation",
- "Read pre-processing",
- "Sequence alignment",
- "Annotation",
- "Validation",
- "Primer removal",
+ "Statistical calculation",
+ "Sequencing quality control",
"Sequence composition calculation",
- "RNA-Seq quantification",
- "Sequence trimming",
- "Gene functional annotation"
+ "Data handling",
+ "Primer removal",
+ "Sequence alignment",
+ "Gene functional annotation",
+ "Sequence trimming"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -846839,7 +786644,6 @@
"inexact_supported_servers": [
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org (Main)"
],
@@ -846860,7 +786664,7 @@
"Perform an analysis using a workflow from WorkflowHub",
"Visualise and interpret the results with MINERVA"
],
- "pageviews": 283,
+ "pageviews": 287,
"priority": 2,
"pub_date": "2024-03-28",
"questions": [
@@ -846869,26 +786673,26 @@
],
"short_id": "T00437",
"short_tools": [
- "tp_replace_in_line",
- "Add_a_column1",
"tp_sort_header_tool",
- "tp_sorted_uniq",
- "limma_voom",
- "multiqc",
- "annotatemyids",
- "rseqc_geneBody_coverage",
- "join1",
"Cut1",
+ "multiqc",
"Grep1",
+ "__EXTRACT_DATASET__",
+ "tp_replace_in_line",
+ "rseqc_geneBody_coverage",
+ "Add_a_column1",
+ "cutadapt",
+ "annotatemyids",
"collection_column_join",
+ "tp_sorted_uniq",
"featurecounts",
- "fasterq_dump",
- "hisat2",
"fastqc",
- "cutadapt",
- "__EXTRACT_DATASET__",
+ "rseqc_read_distribution",
"goseq",
- "rseqc_read_distribution"
+ "limma_voom",
+ "join1",
+ "fasterq_dump",
+ "hisat2"
],
"slides": false,
"slides_recordings": false,
@@ -846917,11 +786721,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -846956,6 +786755,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -847011,10 +786814,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -847061,11 +786860,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -847110,6 +786904,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -847162,10 +786960,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -847206,10 +787000,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -847252,6 +787042,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -847304,10 +787098,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -847348,10 +787138,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -847394,6 +787180,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -847446,10 +787236,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -847490,10 +787276,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -847536,6 +787318,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -847588,10 +787374,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -847632,10 +787414,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -847678,6 +787456,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -847732,10 +787514,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -847782,11 +787560,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -847832,6 +787605,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -847886,10 +787663,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -847936,11 +787709,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -847986,6 +787754,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -848040,10 +787812,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -848090,11 +787858,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
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{
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"state": "exact",
@@ -848140,6 +787903,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -848200,10 +787967,6 @@
"server": "http://galaxy.interactomix.com/",
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{
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"server": "https://usegalaxy.be/",
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"versions": [
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"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
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},
@@ -848255,18 +788018,6 @@
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{
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@@ -848276,10 +788027,10 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
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"1.5",
- "2.0",
"1.2.0",
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"2.1",
"1.3.1"
@@ -848320,6 +788071,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -848502,6 +788248,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -848558,10 +788308,6 @@
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{
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@@ -848599,8 +788345,8 @@
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{
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{
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"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -848721,10 +788466,6 @@
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@@ -848769,11 +788510,6 @@
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@@ -848819,6 +788555,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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+ "state": "missing"
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{
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@@ -848880,10 +788620,6 @@
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@@ -848995,6 +788726,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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+ "state": "missing"
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{
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"server": "https://usegalaxy.be/",
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+ "state": "missing"
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{
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@@ -849264,11 +788990,6 @@
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{
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@@ -849314,6 +789035,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -849366,10 +789091,6 @@
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{
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{
@@ -849423,20 +789144,15 @@
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{
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@@ -849479,6 +789195,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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{
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@@ -849600,8 +789311,8 @@
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@@ -849644,6 +789355,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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{
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@@ -849699,10 +789414,6 @@
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{
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@@ -849749,16 +789460,16 @@
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},
{
@@ -849766,11 +789477,6 @@
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- "state": "exact",
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{
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@@ -849818,6 +789524,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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},
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -849857,8 +789567,8 @@
"server": "https://galaxytrakr.org/",
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{
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"server": "http://galaxy.interactomix.com/",
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{
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@@ -849925,8 +789631,8 @@
"1.16.8",
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{
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@@ -849991,6 +789692,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -850046,10 +789751,6 @@
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"server": "https://usegalaxy.be/",
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"versions": [
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- "2.6.4.3"
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},
{
@@ -850099,11 +789800,6 @@
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -850154,6 +789850,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -850209,10 +789909,6 @@
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{
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@@ -850262,11 +789958,6 @@
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- "version": "5.0.1+galaxy2"
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{
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"state": "inexact",
@@ -850346,7 +790037,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 87,
- "visitors": 244,
+ "visitors": 248,
"workflows": [
{
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@@ -850404,7 +790095,7 @@
],
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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "BY-COVID: Data Download",
"outputs": [
{
@@ -850629,7 +790320,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Counts\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Lengths\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Column join\"];\n 0 -->|output| 3;\n 4[\"Extract dataset\"];\n 2 -->|output| 4;\n 5[\"countdata\"];\n 3 -->|tabular_output| 5;\n e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5[\"Output\\ncount_data\"];\n 5 --> e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5;\n style e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5 stroke:#2c3143,stroke-width:4px;\n 6[\"annodata\"];\n 3 -->|tabular_output| 6;\n 7[\"Replace Text\"];\n 5 -->|outfile| 7;\n 8[\"limma DEG analysis\"];\n 6 -->|out_tab| 8;\n 7 -->|outfile| 8;\n 1 -->|output| 8;\n 1c8d7950-1003-4c86-9986-c6ed1264cd8b[\"Output\\nlimma_report\"];\n 8 --> 1c8d7950-1003-4c86-9986-c6ed1264cd8b;\n style 1c8d7950-1003-4c86-9986-c6ed1264cd8b stroke:#2c3143,stroke-width:4px;\n 9[\"Extract dataset\"];\n 8 -->|outTables| 9;\n 10[\"MINERVA Formatting\"];\n 9 -->|output| 10;\n 9ce4f48b-e742-4b7c-9bde-5d51f11068d3[\"Output\\nminerva_table\"];\n 10 --> 9ce4f48b-e742-4b7c-9bde-5d51f11068d3;\n style 9ce4f48b-e742-4b7c-9bde-5d51f11068d3 stroke:#2c3143,stroke-width:4px;\n 11[\"Join two Datasets\"];\n 9 -->|output| 11;\n 4 -->|output| 11;\n 12[\"Compute\"];\n 11 -->|out_file1| 12;\n 13[\"Cut\"];\n 12 -->|out_file1| 13;\n 14[\"Unique\"];\n 13 -->|out_file1| 14;\n 15[\"Cut\"];\n 14 -->|outfile| 15;\n 16[\"Cut\"];\n 14 -->|outfile| 16;\n 17[\"goseq\"];\n 15 -->|out_file1| 17;\n 16 -->|out_file1| 17;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "mRNA-Seq BY-COVID Pipeline: Analysis",
"outputs": [
{
@@ -850918,7 +790609,7 @@
],
"license": "GPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nmRNA-Seq Reads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nUCSC Genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"FastQC\"];\n 0 -->|output| 2;\n 3[\"Cutadapt\"];\n 0 -->|output| 3;\n 4[\"FastQC\"];\n 3 -->|out1| 4;\n 5[\"HISAT2\"];\n 3 -->|out1| 5;\n 6[\"featureCounts\"];\n 5 -->|output_alignments| 6;\n 5cb5bd5d-df81-4463-8002-e89551780f01[\"Output\\noutput_feature_lengths\"];\n 6 --> 5cb5bd5d-df81-4463-8002-e89551780f01;\n style 5cb5bd5d-df81-4463-8002-e89551780f01 stroke:#2c3143,stroke-width:4px;\n 5dec13e1-0011-472c-a72d-6715fe55c23c[\"Output\\noutput_short\"];\n 6 --> 5dec13e1-0011-472c-a72d-6715fe55c23c;\n style 5dec13e1-0011-472c-a72d-6715fe55c23c stroke:#2c3143,stroke-width:4px;\n 7[\"Read Distribution\"];\n 5 -->|output_alignments| 7;\n 1 -->|output| 7;\n 8[\"Gene Body Coverage BAM\"];\n 5 -->|output_alignments| 8;\n 1 -->|output| 8;\n 9[\"Multi QC raw reads\"];\n 2 -->|text_file| 9;\n 4 -->|text_file| 9;\n 3 -->|report| 9;\n 5 -->|summary_file| 9;\n 7 -->|output| 9;\n 8 -->|outputtxt| 9;\n 6 -->|output_summary| 9;\n 9217af4e-e34c-4a49-9d67-4b3df511ac2c[\"Output\\nhtml_report\"];\n 9 --> 9217af4e-e34c-4a49-9d67-4b3df511ac2c;\n style 9217af4e-e34c-4a49-9d67-4b3df511ac2c stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "mRNA-Seq BY-COVID Pipeline: Counts",
"outputs": [
{
@@ -851434,22 +791125,21 @@
],
"dir": "topics/transcriptomics/tutorials/de-novo",
"edam_operation": [
- "Statistical calculation",
+ "RNA-Seq quantification",
"RNA-Seq analysis",
- "Sequencing quality control",
- "Read summarisation",
"Sequence annotation",
- "Sequence alignment",
- "Differential gene expression analysis",
+ "Read summarisation",
+ "Transcriptome assembly",
+ "Statistical calculation",
+ "Sequencing quality control",
"Sequence composition calculation",
- "RNA-Seq quantification",
- "Transcriptome assembly"
+ "Differential gene expression analysis",
+ "Sequence alignment"
],
"edam_topic": [],
"exact_supported_servers": [
"Galaxy@AuBi",
"UseGalaxy.be",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -851479,7 +791169,7 @@
"Reconstruction of transcripts without reference transcriptome (de novo)",
"Analysis of differentially expressed genes"
],
- "pageviews": 25074,
+ "pageviews": 25128,
"priority": 3,
"pub_date": "2017-02-19",
"questions": [
@@ -851502,16 +791192,16 @@
],
"short_id": "T00289",
"short_tools": [
+ "Filter1",
"deseq2",
- "fastqc",
+ "gffcompare",
"featurecounts",
- "deeptools_bam_coverage",
- "Filter1",
- "trimmomatic",
- "hisat2",
"stringtie",
+ "fastqc",
+ "trimmomatic",
"stringtie_merge",
- "gffcompare"
+ "hisat2",
+ "deeptools_bam_coverage"
],
"slides": false,
"slides_recordings": false,
@@ -851528,11 +791218,6 @@
"url": "https://usegalaxy.be/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -851584,6 +791269,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -851639,10 +791328,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -851689,11 +791374,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -851738,6 +791418,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -851790,10 +791474,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -851834,10 +791514,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -851880,6 +791556,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -851936,10 +791616,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -851990,25 +791666,20 @@
"versions": [
"3.5.1.0.0",
"3.5.4+galaxy0",
- "3.0.2.0",
- "2.5.1.1.0",
"3.3.2.0.0",
+ "2.5.1.1.0",
+ "3.0.2.0",
"3.5.2+galaxy0",
"2.4.1.0",
"2.2.3.0",
"2.1.0.0",
+ "2.5.0.0",
"2.0.1.0",
- "2.5.7.0",
- "2.2.2.0",
"3.0.1.0",
- "2.5.0.0"
+ "2.5.7.0",
+ "2.2.2.0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.3.0.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -852057,6 +791728,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852114,10 +791789,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -852168,9 +791839,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -852181,11 +791852,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -852231,6 +791897,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852285,10 +791955,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -852341,18 +792007,13 @@
"state": "exact",
"version": "2.11.40.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.11.40.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.11.40.6+galaxy1",
- "2.11.40.6+galaxy2",
- "2.11.40.7+galaxy0"
+ "2.11.40.7+galaxy0",
+ "2.11.40.6+galaxy2"
]
},
{
@@ -852395,6 +792056,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852449,10 +792114,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -852505,18 +792166,13 @@
"state": "exact",
"version": "1.6.4+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.6.4+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.0.1",
- "2.0.1+galaxy1",
"1.6.4+galaxy2",
+ "2.0.1+galaxy1",
"2.0.1+galaxy2"
]
},
@@ -852560,6 +792216,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852613,10 +792273,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -852660,11 +792316,6 @@
"state": "exact",
"version": "0.11.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.11.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -852710,6 +792361,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852764,10 +792419,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -852814,11 +792465,6 @@
"state": "exact",
"version": "2.1.0+galaxy5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.0+galaxy5"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -852864,6 +792510,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -852917,10 +792567,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -852969,11 +792615,6 @@
"state": "exact",
"version": "1.3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -852996,9 +792637,9 @@
"2.1.1",
"1.3.4",
"2.2.1+galaxy1",
- "1.3.3.1",
"2.1.7+galaxy1",
"2.1.7",
+ "1.3.3.1",
"2.2.3+galaxy0"
]
},
@@ -853032,6 +792673,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -853085,10 +792730,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -853137,18 +792778,13 @@
"state": "exact",
"version": "1.3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"2.1.1",
- "2.1.7+galaxy1",
- "2.1.7"
+ "2.1.7",
+ "2.1.7+galaxy1"
]
},
{
@@ -853161,13 +792797,13 @@
"state": "inexact",
"versions": [
"2.2.1+galaxy0",
- "1.3.4",
- "1.3.3",
"2.1.1",
+ "1.3.3",
+ "1.3.4",
"2.2.1+galaxy1",
- "2.1.7+galaxy1",
+ "2.1.7",
"2.2.3+galaxy0",
- "2.1.7"
+ "2.1.7+galaxy1"
]
},
{
@@ -853200,6 +792836,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -853233,8 +792873,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.38.1",
"0.39+galaxy0",
+ "0.38.1",
"0.36.4"
]
},
@@ -853258,10 +792898,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -853309,31 +792945,26 @@
"0.38.1",
"0.36.4",
"0.32.3",
+ "0.36.0",
"0.32.1",
- "0.32.2",
- "0.36.0"
+ "0.32.2"
]
},
{
"server": "https://usegalaxy.eu",
"state": "inexact",
"versions": [
- "0.38.1",
"0.39+galaxy0",
+ "0.38.1",
"0.36.4",
"0.39+galaxy2",
"0.36.5",
"0.32.3",
+ "0.36.0",
"0.32.1",
- "0.32.2",
- "0.36.0"
+ "0.32.2"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.38.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -853399,8 +793030,8 @@
"video": true,
"video_versions": 1,
"video_view": 0,
- "visit_duration": 152,
- "visitors": 14215,
+ "visit_duration": 151,
+ "visitors": 14261,
"workflows": [
{
"creators": [],
@@ -853762,7 +793393,7 @@
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@@ -856517,23 +795769,23 @@
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"Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles."
],
- "pageviews": 13949,
+ "pageviews": 14009,
"pub_date": "2017-02-16",
"questions": [
"How does frequency of mitochondrial polymorphisms change from mother to child?"
],
"short_id": "T00314",
"short_tools": [
- "picard_MarkDuplicates",
- "fastqc",
- "bamFilter",
+ "vcf2tsv",
+ "Cut1",
"freebayes",
"bamleftalign",
- "vcf2tsv",
+ "fastqc",
"bwa_mem",
- "picard_MergeSamFiles",
- "Cut1",
- "vcffilter2"
+ "vcffilter2",
+ "picard_MarkDuplicates",
+ "bamFilter",
+ "picard_MergeSamFiles"
],
"slides": false,
"slides_recordings": false,
@@ -856550,11 +795802,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -856601,6 +795848,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -856656,10 +795907,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -856706,11 +795953,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -856755,6 +795997,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -856807,10 +796053,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -856851,10 +796093,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -856897,6 +796135,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -856953,10 +796195,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -857002,11 +796240,6 @@
"state": "exact",
"version": "2.4.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857052,6 +796285,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857109,10 +796346,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857160,11 +796393,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857213,6 +796441,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857270,10 +796502,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857324,9 +796552,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -857337,11 +796565,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857387,6 +796610,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857445,10 +796672,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857497,11 +796720,6 @@
"state": "exact",
"version": "1.1.0.46-0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0.46-0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857547,6 +796765,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857603,10 +796825,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857655,11 +796873,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857705,6 +796918,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857763,10 +796980,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857815,11 +797028,6 @@
"state": "exact",
"version": "1.1.0.46-0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0.46-0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -857865,6 +797073,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -857921,10 +797133,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -857973,11 +797181,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -858023,6 +797226,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -858080,10 +797287,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -858133,11 +797336,6 @@
"state": "exact",
"version": "2.18.2.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -858183,6 +797381,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -858237,10 +797439,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -858287,11 +797485,6 @@
"state": "exact",
"version": "2.18.2.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -858337,6 +797530,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -858393,10 +797590,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -858440,11 +797633,6 @@
"state": "exact",
"version": "1.0.0_rc1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0_rc1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -858490,6 +797678,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -858546,10 +797738,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -858596,11 +797784,6 @@
"state": "exact",
"version": "1.0.0_rc1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.0_rc1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -858670,7 +797853,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 130,
- "visitors": 7390,
+ "visitors": 7411,
"workflows": [
{
"creators": [],
@@ -858875,7 +798058,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nraw_child-ds-1.fq\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nraw_child-ds-2.fq\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nraw_mother-ds-1.fq\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nraw_mother-ds-2.fq\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"FastQC\"];\n 0 -->|output| 4;\n 5[\"FastQC\"];\n 1 -->|output| 5;\n 6[\"Map with BWA-MEM\"];\n 0 -->|output| 6;\n 1 -->|output| 6;\n 7[\"FastQC\"];\n 2 -->|output| 7;\n 8[\"FastQC\"];\n 3 -->|output| 8;\n 9[\"Map with BWA-MEM\"];\n 2 -->|output| 9;\n 3 -->|output| 9;\n 10[\"MergeSamFiles\"];\n 9 -->|bam_output| 10;\n 6 -->|bam_output| 10;\n 11[\"MarkDuplicates\"];\n 10 -->|outFile| 11;\n 12[\"BamLeftAlign\"];\n 11 -->|outFile| 12;\n 13[\"Filter\"];\n 12 -->|output_bam| 13;\n 14[\"FreeBayes\"];\n 13 -->|out_file1| 14;\n 15[\"VCFfilter:\"];\n 14 -->|output_vcf| 15;\n 16[\"VCFtoTab-delimited:\"];\n 15 -->|out_file1| 16;\n 17[\"Cut\"];\n 16 -->|out_file1| 17;\n f2e84a79-a71f-4b5f-a526-55d8cd472a05[\"Output\\ncut_variants\"];\n 17 --> f2e84a79-a71f-4b5f-a526-55d8cd472a05;\n style f2e84a79-a71f-4b5f-a526-55d8cd472a05 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Calling variants in non-diploid systems",
"outputs": [
{
@@ -859858,6 +799041,20 @@
"tool_panel_section_label": "Mapping",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "bwa",
+ "owner": "devteam",
+ "revisions": "2477830927ec",
+ "tool_panel_section_label": "Mapping",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
+ {
+ "name": "fastqc",
+ "owner": "devteam",
+ "revisions": "2c64fded1286",
+ "tool_panel_section_label": "FASTA/FASTQ",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "freebayes",
"owner": "devteam",
@@ -859865,6 +799062,13 @@
"tool_panel_section_label": "Variant Calling",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "freebayes",
+ "owner": "devteam",
+ "revisions": "3e954e7125bf",
+ "tool_panel_section_label": "Variant Calling",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "allele_counts",
"owner": "nick",
@@ -859872,6 +799076,13 @@
"tool_panel_section_label": "Variant Calling",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "allele_counts",
+ "owner": "nick",
+ "revisions": "cf2af5c3118c",
+ "tool_panel_section_label": "Variant Calling",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "dunovo",
"owner": "nick",
@@ -859886,6 +799097,13 @@
"tool_panel_section_label": "Du Novo",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "dunovo",
+ "owner": "nick",
+ "revisions": "0f8e0dc73d1d",
+ "tool_panel_section_label": "Du Novo",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "dunovo",
"owner": "nick",
@@ -859893,6 +799111,13 @@
"tool_panel_section_label": "Du Novo",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "dunovo",
+ "owner": "nick",
+ "revisions": "0f8e0dc73d1d",
+ "tool_panel_section_label": "Du Novo",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "dunovo",
"owner": "nick",
@@ -859900,36 +799125,31 @@
"tool_panel_section_label": "Du Novo",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
},
+ {
+ "name": "dunovo",
+ "owner": "nick",
+ "revisions": "0f8e0dc73d1d",
+ "tool_panel_section_label": "Du Novo",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
{
"name": "sequence_content_trimmer",
"owner": "nick",
"revisions": "7f170cb06e2e",
"tool_panel_section_label": "Du Novo",
"tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+ },
+ {
+ "name": "sequence_content_trimmer",
+ "owner": "nick",
+ "revisions": "464aee13e2df",
+ "tool_panel_section_label": "Du Novo",
+ "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
}
]
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@@ -861851,7 +802056,7 @@
{
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"state": "exact",
- "version": "0.1"
+ "version": "0.2.3"
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{
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@@ -861862,27 +802067,32 @@
"state": "missing"
}
],
- "version": "0.1"
+ "version": "0.2.3"
}
]
},
"symlink": null,
- "tags": [
- "work-in-progress"
- ],
"time_estimation": "3h",
"title": "Calling very rare variants",
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"toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+ "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
+ "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1",
"toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0",
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"toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2",
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"toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/2.15",
+ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/3.0.2",
"toolshed.g2.bx.psu.edu/repos/nick/dunovo/dunovo/2.15",
+ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/dunovo/3.0.2",
"toolshed.g2.bx.psu.edu/repos/nick/dunovo/make_families/2.15",
- "toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.1"
+ "toolshed.g2.bx.psu.edu/repos/nick/dunovo/make_families/3.0.2",
+ "toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.1",
+ "toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.2.3"
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"topic_name_human": "Variant Analysis",
@@ -861899,12 +802109,12 @@
"hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dunovo/tutorial.json",
"slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dunovo/tutorial.json"
},
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+ "version": 21,
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 100,
- "visitors": 1528,
+ "visit_duration": 101,
+ "visitors": 1536,
"workflows": [
{
"creators": [],
@@ -862007,7 +802217,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nSRR1799908_forward\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSRR1799908_reverse\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Du Novo: Make families\"];\n 0 -->|output| 2;\n 1 -->|output| 2;\n 3[\"Du Novo: Correct barcodes\"];\n 2 -->|output| 3;\n 4[\"Du Novo: Align families\"];\n 3 -->|output| 4;\n 5[\"Du Novo: Make consensus reads\"];\n 4 -->|output| 5;\n 6[\"DCS: Sequence Content Trimmer\"];\n 5 -->|dcs1| 6;\n 5 -->|dcs2| 6;\n 7[\"SSCS: Sequence Content Trimmer\"];\n 5 -->|sscs1| 7;\n 5 -->|sscs2| 7;\n 75dfe52d-711e-4826-ba9b-b4feed30f5bf[\"Output\\n\"];\n 7 --> 75dfe52d-711e-4826-ba9b-b4feed30f5bf;\n style 75dfe52d-711e-4826-ba9b-b4feed30f5bf stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Du Novo GTN Tutorial - Make Consensus Sequences",
"outputs": [
{
@@ -862354,7 +802564,7 @@
],
"license": null,
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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Du Novo GTN Tutorial - Variant Calling",
"outputs": [
{
@@ -862547,7 +802757,7 @@
"workflowhub_id": "1089"
}
],
- "zenodo_link": ""
+ "zenodo_link": "https://doi.org/10.5281/zenodo.3554549"
},
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@@ -862664,19 +802874,6 @@
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- "hexylena",
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- "shiltemann"
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@@ -862694,167 +802891,20 @@
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"page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
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- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
- "orcid": "0000-0002-6100-4385",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
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- "deNBI",
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- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
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- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
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- "fediverse_flavor": "mastodon",
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- "elixir-europe"
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- "bio": "Researcher at Erasmus Medical Center",
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- "fediverse": "https://mstdn.science/@shiltemann",
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- "maintainer_contact": "gitter",
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}
],
"dir": "topics/variant-analysis/tutorials/somatic-variants",
"edam_operation": [
- "Data handling",
- "Variant calling",
+ "Validation",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment analysis",
- "Sequence alignment",
- "Validation",
"Sequence composition calculation",
- "Read mapping",
+ "Data handling",
+ "Variant calling",
+ "Sequence alignment analysis",
"Generation",
+ "Read mapping",
+ "Sequence alignment",
"Genome indexing"
],
"edam_topic": [],
@@ -862870,8 +802920,7 @@
"hands_on": true,
"id": "variant-analysis/somatic-variants",
"inexact_supported_servers": [
- "UseGalaxy.cz",
- "UseGalaxy.fr"
+ "UseGalaxy.cz"
],
"js_requirements": {
"mathjax": null,
@@ -862892,7 +802941,7 @@
"Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases",
"Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians"
],
- "pageviews": 22711,
+ "pageviews": 22757,
"pub_date": "2019-03-13",
"questions": [
"What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?",
@@ -862901,21 +802950,21 @@
],
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- "fastqc",
- "bamFilter",
- "samtools_calmd",
- "gemini_annotate",
- "multiqc",
"samtools_rmdup",
+ "gemini_annotate",
+ "gemini_query",
+ "snpEff",
+ "bg_column_arrange_by_header",
+ "fastqc",
+ "bwa_mem",
+ "tp_easyjoin_tool",
"bamleftalign",
+ "multiqc",
"trimmomatic",
- "snpEff",
- "gemini_query",
- "varscan_somatic",
+ "bamFilter",
"gemini_load",
- "bwa_mem",
- "bg_column_arrange_by_header"
+ "samtools_calmd",
+ "varscan_somatic"
],
"slides": false,
"slides_recordings": false,
@@ -862953,11 +803002,6 @@
"name": "UseGalaxy.cz",
"url": "https://usegalaxy.cz/",
"usegalaxy": false
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
}
]
},
@@ -862983,6 +803027,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -863038,10 +803086,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -863088,11 +803132,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -863137,6 +803176,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863190,10 +803233,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
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"state": "missing"
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- "version": "0.2"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -863287,6 +803321,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863345,10 +803383,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
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- "version": "1.1.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -863448,6 +803477,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863504,10 +803537,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -863553,11 +803582,6 @@
"state": "exact",
"version": "2.4.1"
},
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -863603,6 +803627,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863660,10 +803688,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -863711,11 +803735,6 @@
"state": "exact",
"version": "0.7.17.1"
},
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- "state": "exact",
- "version": "0.7.17.1"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -863764,6 +803783,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863821,10 +803844,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -863875,9 +803894,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -863888,11 +803907,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -863938,6 +803952,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -863994,10 +804012,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -864046,11 +804060,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -864096,6 +804105,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -864149,10 +804162,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -864198,11 +804207,6 @@
"state": "exact",
"version": "2.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -864248,6 +804252,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -864301,10 +804309,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -864349,11 +804353,6 @@
"state": "exact",
"version": "2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -864400,152 +804399,7 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "missing"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "missing"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "missing"
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
- }
- ],
- "version": "0.20.1+galaxy2"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
- "servers": [
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- "server": "http://apostl.moffitt.org/",
- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
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- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -864600,14 +804454,9 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
- "state": "exact",
- "version": "0.20.1+galaxy2"
+ "state": "missing"
},
{
"server": "https://neo.engr.uconn.edu/",
@@ -864649,7 +804498,147 @@
"version": "0.20.1+galaxy2"
},
{
- "server": "https://usegalaxy.fr/",
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "0.20.1+galaxy2"
+ },
+ {
+ "server": "https://usegalaxy.eu",
"state": "exact",
"version": "0.20.1+galaxy2"
},
@@ -864698,6 +804687,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -864750,10 +804743,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -864799,11 +804788,6 @@
"state": "exact",
"version": "0.20.1+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -864849,6 +804833,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -864874,9 +804862,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -864913,10 +804901,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -864966,11 +804950,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -865016,6 +804995,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -865069,10 +805052,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -865117,11 +805096,6 @@
"state": "exact",
"version": "4.3+T.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+T.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -865167,6 +805141,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -865219,10 +805197,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -865266,11 +805240,6 @@
"state": "exact",
"version": "2.4.3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.4.3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -865316,6 +805285,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -865340,10 +805313,10 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "0.36.6",
"0.38.0",
- "0.38.1",
"0.39+galaxy0",
- "0.36.6"
+ "0.38.1"
]
},
{
@@ -865354,8 +805327,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.38.1",
"0.39+galaxy0",
+ "0.38.1",
"0.36.4"
]
},
@@ -865379,10 +805352,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -865430,9 +805399,9 @@
"0.38.1",
"0.36.4",
"0.32.3",
+ "0.36.0",
"0.32.1",
- "0.32.2",
- "0.36.0"
+ "0.32.2"
]
},
{
@@ -865440,17 +805409,6 @@
"state": "exact",
"version": "0.36.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.38.0",
- "0.38.1",
- "0.39+galaxy0",
- "0.39+galaxy2",
- "0.39+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -865514,8 +805472,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 151,
- "visitors": 12102,
+ "visit_duration": 152,
+ "visitors": 12128,
"workflows": [
{
"creators": [],
@@ -865526,7 +805484,7 @@
"report": null,
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@@ -865851,8 +805809,8 @@
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+ "modified": "2024-12-13 13:26:20 +0000",
"name": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
"outputs": [
{
@@ -865895,7 +805853,7 @@
{
"label": "gene_report_output",
"output_name": "output",
- "uuid": "2fce929a-ce26-4a91-8678-93752318dba6"
+ "uuid": "fd23fd95-5d79-45ef-aa44-37fb803c1ddf"
}
]
}
@@ -866256,14 +806214,14 @@
"Multiple sequence alignment",
"Global alignment",
"Sequencing quality control",
+ "Local alignment",
+ "Sequence contamination filtering",
"Sequence alignment analysis",
- "Sequence alignment",
- "Sequence analysis",
- "Read mapping",
- "Genome indexing",
"Generation",
- "Sequence contamination filtering",
- "Local alignment"
+ "Read mapping",
+ "Sequence analysis",
+ "Sequence alignment",
+ "Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -866294,7 +806252,7 @@
"Construct a sample consensus genome from mapped reads",
"Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
],
- "pageviews": 775,
+ "pageviews": 784,
"pub_date": "2023-05-15",
"questions": [
"Which special challenges does one encounter during sequence data analysis of pox viruses?",
@@ -866313,28 +806271,28 @@
],
"short_id": "T00347",
"short_tools": [
- "datamash_ops",
- "Add_a_column1",
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- "__APPLY_RULES__",
- "EMBOSS: maskseq51",
- "rbc_mafft",
- "mimodd_info",
- "compose_text_param",
- "param_value_from_file",
"Cut1",
- "ivar_trim",
- "__ZIP_COLLECTION__",
+ "fastp",
+ "fasta_compute_length",
"Grep1",
- "ivar_consensus",
"qualimap_bamqc",
- "fasta_regex_finder",
- "fatovcf",
+ "mimodd_info",
+ "upload1",
+ "Add_a_column1",
"bwa_mem",
+ "ivar_consensus",
+ "rbc_mafft",
+ "EMBOSS: maskseq51",
+ "ivar_trim",
+ "compose_text_param",
+ "fatovcf",
"samtools_merge",
- "fasta_compute_length",
- "samtools_view"
+ "samtools_view",
+ "datamash_ops",
+ "__ZIP_COLLECTION__",
+ "__APPLY_RULES__",
+ "fasta_regex_finder",
+ "param_value_from_file"
],
"slides": false,
"slides_recordings": false,
@@ -866377,6 +806335,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -866432,10 +806394,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -866482,11 +806440,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -866531,6 +806484,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -866583,10 +806540,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -866627,10 +806580,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -866673,6 +806622,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -866725,10 +806678,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -866769,10 +806718,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -866815,6 +806760,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -866867,10 +806816,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -866911,10 +806856,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -866957,6 +806898,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -867009,10 +806954,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -867053,10 +806994,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -867099,6 +807036,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867151,10 +807092,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -867195,10 +807132,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -867241,6 +807174,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867300,10 +807237,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -867351,11 +807284,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -867402,6 +807330,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867462,10 +807394,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -867499,9 +807427,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.3.0",
"1.5",
"1.2.0",
+ "1.3.0",
"1.1.0"
]
},
@@ -867515,11 +807443,6 @@
"state": "exact",
"version": "2.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -867565,6 +807488,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867618,10 +807545,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -867666,11 +807589,6 @@
"state": "exact",
"version": "5.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -867716,6 +807634,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867769,10 +807691,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -867817,11 +807735,6 @@
"state": "exact",
"version": "1.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -867867,6 +807780,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -867919,10 +807836,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -867966,11 +807879,6 @@
"state": "exact",
"version": "0.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -868015,6 +807923,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -868074,10 +807986,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -868132,11 +808040,6 @@
"state": "exact",
"version": "1.1.0+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -868183,167 +808086,166 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
- },
- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
- },
- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
- "0.23.4+galaxy0"
- ]
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "inexact",
- "versions": [
- "0.20.1+galaxy0",
- "0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
- "0.19.3.2",
- "0.19.5"
- ]
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- },
- {
- "server": "https://viralvariant.anses.fr/",
- "state": "exact",
- "version": "0.23.2+galaxy0"
- }
- ],
- "version": "0.23.2+galaxy0"
- },
- {
- "id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
- "servers": [
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- "state": "missing"
- },
- {
- "server": "http://smile.hku.hk/SARGs",
- "state": "missing"
- },
- {
- "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
- "state": "missing"
- },
- {
- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "missing"
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
+ "state": "missing"
+ },
+ {
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
+ "0.23.4+galaxy0"
+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "inexact",
+ "versions": [
+ "0.20.1+galaxy0",
+ "0.19.5+galaxy1",
+ "0.19.3.2",
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "exact",
+ "version": "0.23.2+galaxy0"
+ }
+ ],
+ "version": "0.23.2+galaxy0"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
@@ -868401,10 +808303,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -868439,8 +808337,8 @@
"state": "inexact",
"versions": [
"1.2+galaxy0",
- "1.0.1+galaxy0",
- "1.2.2+galaxy0"
+ "1.2.2+galaxy0",
+ "1.0.1+galaxy0"
]
},
{
@@ -868453,11 +808351,6 @@
"state": "exact",
"version": "1.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -868506,6 +808399,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -868538,9 +808435,9 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.3.1+galaxy3",
"1.3.1+galaxy4",
- "1.3.1+galaxy2"
+ "1.3.1+galaxy2",
+ "1.3.1+galaxy3"
]
},
{
@@ -868563,10 +808460,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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{
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"state": "exact",
@@ -868600,9 +808493,9 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "1.0.1+galaxy0",
"1.2+galaxy0",
- "1.2.2+galaxy0"
+ "1.2.2+galaxy0",
+ "1.0.1+galaxy0"
]
},
{
@@ -868615,18 +808508,13 @@
"state": "exact",
"version": "1.4.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.4.2+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "1.3.1+galaxy3",
"1.3.1+galaxy4",
"1.3.1+galaxy2",
+ "1.3.1+galaxy3",
"1.3.1+galaxy0",
"1.3.1+galaxy1",
"1.2.2+galaxy1"
@@ -868672,6 +808560,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -868728,10 +808620,6 @@
"server": "http://galaxy.interactomix.com/",
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -868778,11 +808666,6 @@
"state": "exact",
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},
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- "state": "exact",
- "version": "2.2.2d+galaxy3"
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -868828,6 +808711,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -868883,10 +808770,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -868932,11 +808815,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -868982,6 +808860,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -869006,8 +808888,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -869041,10 +808923,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -869094,11 +808972,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -869144,6 +809017,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -869196,10 +809073,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -869242,10 +809115,6 @@
"state": "exact",
"version": "426+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -869293,6 +809162,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -869345,10 +809218,6 @@
"server": "http://galaxy.interactomix.com/",
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- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -869391,10 +809260,6 @@
"state": "exact",
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -869438,6 +809303,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -869474,8 +809343,8 @@
"state": "inexact",
"versions": [
"7.221.3",
- "7.508+galaxy0",
- "7.475+galaxy0"
+ "7.475+galaxy0",
+ "7.508+galaxy0"
]
},
{
@@ -869498,10 +809367,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -869554,11 +809419,6 @@
"state": "exact",
"version": "7.520+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "7.520+galaxy0"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -869607,6 +809467,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -869662,10 +809526,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -869709,10 +809569,6 @@
"state": "exact",
"version": "0.1.8_1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -869764,6 +809620,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -869816,10 +809676,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -869860,10 +809716,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -869935,8 +809787,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 173,
- "visitors": 646,
+ "visit_duration": 170,
+ "visitors": 655,
"workflows": [
{
"creators": [
@@ -870033,7 +809885,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Select pool1 primers\"];\n 0 -->|output| 2;\n 3[\"Select pool2 primers\"];\n 0 -->|output| 3;\n 4[\"Compute sequence length\"];\n 1 -->|output| 4;\n 5[\"Datamash\"];\n 2 -->|out_file1| 5;\n 6[\"Datamash\"];\n 3 -->|out_file1| 6;\n 7[\"Cut\"];\n 4 -->|output| 7;\n 8[\"Compute\"];\n 5 -->|out_file| 8;\n 9[\"Get start position of Pool2\"];\n 6 -->|out_file| 9;\n 10[\"Get end position of sequence\"];\n 7 -->|out_file1| 10;\n 11[\"Get end position of Pool1\"];\n 8 -->|out_file1| 11;\n 12[\"Compose text parameter value\"];\n 9 -->|text_param| 12;\n 13[\"Compose text parameter value\"];\n 11 -->|text_param| 13;\n 10 -->|text_param| 13;\n 14[\"Mask Reference for Pool2\"];\n 1 -->|output| 14;\n 12 -->|out1| 14;\n af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n 14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n 15[\"Mask Reference for Pool1\"];\n 1 -->|output| 15;\n 13 -->|out1| 15;\n 0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n 15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "pox-virus-tiled-amplicon-ref-masking",
"outputs": [
{
@@ -870242,21 +810094,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: freebayes\n owner: devteam\n revisions: 156b60c1530f\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vcfallelicprimitives\n owner: devteam\n revisions: f49b23b41a12\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_db_info\n owner: iuc\n revisions: 4c5f4e9b1931\n tool_panel_section_label: Gemini\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n owner: iuc\n revisions: cf61daf064fe\n tool_panel_section_label: Gemini\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_query\n owner: iuc\n revisions: 666f60a9331a\n tool_panel_section_label: Gemini\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n owner: iuc\n revisions: 5c7b70713fb5\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n owner: iuc\n revisions: 68693743661e\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json",
- "contributions": {
- "authorship": [
- "nekrut",
- "nsoranzo"
- ],
- "reviewing": [
- "bgruening",
- "nsoranzo",
- "hexylena",
- "shiltemann",
- "willdurand",
- "bebatut",
- "njall"
- ]
- },
"contributors": [
{
"email": "anton@nekrut.org",
@@ -870283,164 +810120,13 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
"twitter": "NicolaSoranzo",
"url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
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- "earlham",
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
- },
- {
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- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "id": "willdurand",
- "joined": "2017-09",
- "name": "William Durand",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/willdurand.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/variant-analysis/tutorials/dip",
"edam_operation": [
- "Genetic variation analysis",
"Sequence analysis",
"Variant calling",
+ "Genetic variation analysis",
"Statistical calculation"
],
"edam_topic": [],
@@ -870454,7 +810140,6 @@
"inexact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -870475,7 +810160,7 @@
"objectives": [
"Identification of genetic variations using variant calling"
],
- "pageviews": 23020,
+ "pageviews": 23049,
"pub_date": "2017-02-20",
"questions": [
"How to find variable sites in diploid genomes?"
@@ -870483,12 +810168,12 @@
"short_id": "T00309",
"short_tools": [
"gemini_db_info",
+ "vcfallelicprimitives",
+ "gemini_query",
+ "snpEff",
"freebayes",
"snpEff_download",
- "snpEff",
- "gemini_query",
- "gemini_load",
- "vcfallelicprimitives"
+ "gemini_load"
],
"slides": false,
"slides_recordings": false,
@@ -870512,11 +810197,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -870551,6 +810231,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -870606,10 +810290,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -870656,11 +810336,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -870705,6 +810380,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -870763,10 +810442,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -870815,11 +810490,6 @@
"state": "exact",
"version": "1.1.0.46-0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0.46-0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -870865,6 +810535,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -870918,10 +810592,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -870971,14 +810641,6 @@
"state": "exact",
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},
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- "state": "inexact",
- "versions": [
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- "1.0.0_rc1+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -871030,6 +810692,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -871082,10 +810748,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -871130,14 +810792,7 @@
"server": "https://usegalaxy.eu",
"state": "inexact",
"versions": [
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- "0.18.1.1"
- ]
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
+ "0.18.1.1",
"0.20.1"
]
},
@@ -871187,6 +810842,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -871239,10 +810898,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -871295,13 +810950,6 @@
"0.20.1+galaxy1"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -871351,6 +810999,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -871403,10 +811055,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -871456,14 +811104,6 @@
"0.20.1+galaxy2"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "0.20.1+galaxy2"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -871515,6 +811155,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -871568,10 +811212,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -871616,11 +811256,6 @@
"state": "exact",
"version": "4.3+T.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+T.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -871666,6 +811301,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -871721,10 +811360,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -871779,15 +811414,6 @@
"4.0.0"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "4.3+T.galaxy2",
- "4.3+T.galaxy1",
- "5.2+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -871854,8 +811480,8 @@
"video": false,
"video_versions": 0,
"video_view": 0,
- "visit_duration": 194,
- "visitors": 12927,
+ "visit_duration": 193,
+ "visitors": 12954,
"workflows": [
{
"creators": [],
@@ -871958,7 +811584,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"SnpEff Download\"];\n 2[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"FreeBayes\"];\n 0 -->|output| 3;\n 4[\"VcfAllelicPrimitives:\"];\n 3 -->|output_vcf| 4;\n 5[\"SnpEff eff:\"];\n 4 -->|out_file1| 5;\n 1 -->|snpeff_db| 5;\n 6[\"GEMINI load\"];\n 5 -->|snpeff_output| 6;\n 2 -->|output| 6;\n 7[\"GEMINI_db_info\"];\n 6 -->|outfile| 7;\n 8[\"GEMINI_query2\"];\n 6 -->|outfile| 8;\n 9[\"GEMINI_query1\"];\n 6 -->|outfile| 9;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Diploid",
"outputs": [
{
@@ -872270,20 +811896,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: a6f147a050a2\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n owner: iuc\n revisions: 20f0429a4bfe\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n owner: iuc\n revisions: 20f0429a4bfe\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n owner: wolma\n revisions: f0f2795de2c7\n tool_panel_section_label: MiModD\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n owner: wolma\n revisions: f0f2795de2c7\n tool_panel_section_label: MiModD\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n owner: wolma\n revisions: f0f2795de2c7\n tool_panel_section_label: MiModD\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n owner: wolma\n revisions: f0f2795de2c7\n tool_panel_section_label: MiModD\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n owner: wolma\n revisions: f0f2795de2c7\n tool_panel_section_label: MiModD\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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- "reviewing": [
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- "bgruening",
- "nsoranzo",
- "hexylena",
- "bebatut",
- "wm75",
- "njall"
- ]
- },
"contributors": [
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@@ -872301,167 +811913,6 @@
"orcid": "0000-0002-9464-6640",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
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- "elixir-europe"
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- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
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- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
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- "lon": 4.462
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- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
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- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
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- "lat": 47.997791,
- "lon": 7.842609
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- "matrix": "bgruening:matrix.org",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
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- "elixir_node": "uk",
- "fediverse": "https://mstdn.science/@nsoranzo",
- "fediverse_flavor": "mastodon",
- "id": "nsoranzo",
- "joined": "2017-09",
- "linkedin": "nicola-soranzo-7884125",
- "matrix": "nsoranzo:matrix.org",
- "name": "Nicola Soranzo",
- "orcid": "0000-0003-3627-5340",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
- "twitter": "NicolaSoranzo",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
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- "gallantries",
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- "elixir-europe",
- "elixir-converge"
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- "avans-atgm",
- "uni-freiburg"
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- "location": {
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- "lat": 51.91,
- "lon": 4.46
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- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
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- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
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- "ifb",
- "elixir-europe"
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- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
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- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "id": "njall",
- "joined": "2019-02",
- "name": "Niall Beard",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/njall/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/njall.json"
}
],
"dir": "topics/variant-analysis/tutorials/mapping-by-sequencing",
@@ -872498,7 +811949,7 @@
"Perform variant linkage analyses for phenotypically selected recombinant progeny",
"Filter, annotate and report lists of variants"
],
- "pageviews": 5614,
+ "pageviews": 5627,
"pub_date": "2018-03-07",
"questions": [
"What is mapping-by-sequencing?",
@@ -872506,14 +811957,14 @@
],
"short_id": "T00312",
"short_tools": [
- "tp_find_and_replace",
- "snpEff_download",
- "mimodd_varreport",
- "snpEff",
"mimodd_varcall",
+ "mimodd_map",
+ "snpEff",
"mimodd_varextract",
+ "snpEff_download",
"mimodd_vcf_filter",
- "mimodd_map"
+ "tp_find_and_replace",
+ "mimodd_varreport"
],
"slides": false,
"slides_recordings": false,
@@ -872581,6 +812032,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -872636,10 +812091,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -872686,11 +812137,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -872735,6 +812181,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -872759,8 +812209,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.1.4",
- "1.1.3"
+ "1.1.3",
+ "1.1.4"
]
},
{
@@ -872771,8 +812221,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "1.1.4",
- "1.1.3"
+ "1.1.3",
+ "1.1.4"
]
},
{
@@ -872795,10 +812245,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -872839,8 +812285,8 @@
"server": "https://usegalaxy.cz/",
"state": "inexact",
"versions": [
- "1.1.4",
"1.1.3",
+ "1.1.4",
"1.1.0"
]
},
@@ -872849,17 +812295,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
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- "state": "inexact",
- "versions": [
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- "1.1.3",
- "9.3+galaxy1",
- "1.1.2",
- "9.3+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -872905,6 +812340,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -872960,10 +812399,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -873015,15 +812450,6 @@
"state": "exact",
"version": "4.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "4.3+T.galaxy2",
- "5.2+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -873079,6 +812505,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -873134,10 +812564,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -873187,15 +812613,6 @@
"state": "exact",
"version": "4.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
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- "4.3+T.galaxy1",
- "5.2+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -873252,6 +812669,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -873307,10 +812728,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -873354,10 +812771,6 @@
"state": "exact",
"version": "0.1.8_1"
},
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- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -873409,6 +812822,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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@@ -873566,6 +812975,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -873880,6 +813281,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
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@@ -874048,8 +813445,8 @@
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- "visitors": 3708,
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@@ -874151,7 +813548,7 @@
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- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
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@@ -874280,27 +813677,6 @@
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],
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"edam_operation": [
- "Variant calling",
+ "Genetic variation analysis",
+ "Validation",
"Statistical calculation",
"Sequencing quality control",
- "Sequence alignment",
- "Validation",
- "Genetic variation analysis",
- "Sequence analysis",
"Sequence composition calculation",
- "Read mapping",
+ "Variant calling",
"Generation",
+ "Read mapping",
+ "Sequence analysis",
+ "Sequence alignment",
"Genome indexing"
],
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"exact_supported_servers": [
"UseGalaxy.cz",
"UseGalaxy.eu",
- "UseGalaxy.fr",
"UseGalaxy.org (Main)"
],
"feedback_mean_note": null,
@@ -874654,7 +813825,7 @@
"Jointly call variants and genotypes for a family trio from whole-exome sequencing data",
"Use variant annotation and the observed inheritance pattern of a phenotype to identify candidate causative variants and to prioritize them"
],
- "pageviews": 53335,
+ "pageviews": 53449,
"pub_date": "2016-08-19",
"questions": [
"How do you identify genetic variants in samples based on exome sequencing data?",
@@ -874662,18 +813833,18 @@
],
"short_id": "T00311",
"short_tools": [
- "fastqc",
+ "samtools_rmdup",
+ "snpEff",
"freebayes",
+ "fastqc",
+ "bwa_mem",
"multiqc",
+ "samtools_view",
"snpEff_download",
- "samtools_rmdup",
- "gemini_inheritance",
- "snpEff",
"trimmomatic",
"bcftools_norm",
- "gemini_load",
- "bwa_mem",
- "samtools_view"
+ "gemini_inheritance",
+ "gemini_load"
],
"slides": false,
"slides_recordings": false,
@@ -874690,11 +813861,6 @@
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"usegalaxy": true
},
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{
"name": "UseGalaxy.org (Main)",
"url": "https://usegalaxy.org",
@@ -874741,6 +813907,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -874796,10 +813966,6 @@
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},
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- "url": "http://galaxy.ul.edu.lb/"
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{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -874846,11 +814012,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
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- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
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{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -874895,6 +814056,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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{
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{
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"state": "exact",
@@ -875056,6 +814212,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -875081,8 +814241,8 @@
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+ "0.73+galaxy0"
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{
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"state": "exact",
@@ -875146,8 +814302,8 @@
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"0.72",
- "0.65",
- "0.71"
+ "0.71",
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},
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@@ -875167,12 +814323,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
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+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
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},
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{
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"state": "inexact",
@@ -875238,6 +814389,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -875294,10 +814449,6 @@
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{
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"0.0.2",
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+ "1.0.2.29--1",
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{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -875397,6 +814543,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
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+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -875450,10 +814600,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -875498,11 +814644,6 @@
"state": "exact",
"version": "2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -875548,6 +814689,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -875606,10 +814751,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -875659,11 +814800,6 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -875709,6 +814845,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -875761,10 +814901,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
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- "state": "missing"
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -875808,11 +814944,6 @@
"state": "exact",
"version": "0.20.1"
},
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- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -875858,6 +814989,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -875910,10 +815045,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -875958,11 +815089,6 @@
"state": "exact",
"version": "0.20.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -876008,6 +815134,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -876062,10 +815192,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -876114,11 +815240,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -876129,8 +815250,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -876173,6 +815294,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -876197,8 +815322,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -876232,10 +815357,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -876285,11 +815406,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -876335,6 +815451,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -876390,10 +815510,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -876442,11 +815558,6 @@
"state": "exact",
"version": "4.3+T.galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+T.galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -876494,6 +815605,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -876547,10 +815662,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -876595,11 +815706,6 @@
"state": "exact",
"version": "4.3+T.galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+T.galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -876645,6 +815751,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -876699,10 +815809,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -876742,8 +815848,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.38.0",
"0.36.6",
+ "0.38.0",
"0.39+galaxy2",
"0.36.5",
"0.32.3"
@@ -876759,11 +815865,6 @@
"state": "exact",
"version": "0.38.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.38.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -876828,7 +815929,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 168,
- "visitors": 27856,
+ "visitors": 27945,
"workflows": [
{
"creators": [
@@ -876995,7 +816096,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nFather data\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nMother data\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nProband data\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nPEDigree data\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"Samtools view\"];\n 0 -->|output| 4;\n 5[\"Samtools view\"];\n 1 -->|output| 5;\n 6[\"Samtools view\"];\n 2 -->|output| 6;\n 7[\"RmDup\"];\n 4 -->|outputsam| 7;\n 8[\"RmDup\"];\n 5 -->|outputsam| 8;\n 9[\"RmDup\"];\n 6 -->|outputsam| 9;\n 10[\"FreeBayes\"];\n 7 -->|output1| 10;\n 8 -->|output1| 10;\n 9 -->|output1| 10;\n 11[\"bcftools norm\"];\n 10 -->|output_vcf| 11;\n 12[\"SnpEff eff:\"];\n 11 -->|output_file| 12;\n 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272[\"Output\\nsnpeff_variant_stats\"];\n 12 --> 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272;\n style 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272 stroke:#2c3143,stroke-width:4px;\n 083b9686-5c6d-495f-9257-7243896e64d7[\"Output\\nnormalized_snpeff_annotated_variants\"];\n 12 --> 083b9686-5c6d-495f-9257-7243896e64d7;\n style 083b9686-5c6d-495f-9257-7243896e64d7 stroke:#2c3143,stroke-width:4px;\n 13[\"GEMINI load\"];\n 12 -->|snpeff_output| 13;\n 3 -->|output| 13;\n 14[\"GEMINI inheritance pattern\"];\n 13 -->|outfile| 14;\n c5a64822-3c68-495e-b2fd-4642b1aabb5a[\"Output\\ncandidate_mutations\"];\n 14 --> c5a64822-3c68-495e-b2fd-4642b1aabb5a;\n style c5a64822-3c68-495e-b2fd-4642b1aabb5a stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Exome Seq Training Pre-Mapped W Cached Ref",
"outputs": [
{
@@ -877381,7 +816482,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nfather_R1\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nfather_R2\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nmother_R1\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Dataset\\nmother_R2\"];\n style 3 stroke:#2c3143,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Dataset\\nproband_R1\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\nproband_R2\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"\u2139\ufe0f Input Dataset\\nPEDigree data\"];\n style 6 stroke:#2c3143,stroke-width:4px;\n 7[\"FastQC\"];\n 0 -->|output| 7;\n 8[\"FastQC\"];\n 1 -->|output| 8;\n 9[\"Map with BWA-MEM\"];\n 0 -->|output| 9;\n 1 -->|output| 9;\n 10[\"FastQC\"];\n 2 -->|output| 10;\n 11[\"FastQC\"];\n 3 -->|output| 11;\n 12[\"Map with BWA-MEM\"];\n 2 -->|output| 12;\n 3 -->|output| 12;\n 13[\"FastQC\"];\n 4 -->|output| 13;\n 14[\"FastQC\"];\n 5 -->|output| 14;\n 15[\"Map with BWA-MEM\"];\n 4 -->|output| 15;\n 5 -->|output| 15;\n 16[\"Samtools view\"];\n 9 -->|bam_output| 16;\n 17[\"Samtools view\"];\n 12 -->|bam_output| 17;\n 18[\"MultiQC\"];\n 7 -->|text_file| 18;\n 8 -->|text_file| 18;\n 10 -->|text_file| 18;\n 11 -->|text_file| 18;\n 13 -->|text_file| 18;\n 14 -->|text_file| 18;\n de867748-890a-454c-baf3-6a9313269975[\"Output\\nmultiqc_input_data\"];\n 18 --> de867748-890a-454c-baf3-6a9313269975;\n style de867748-890a-454c-baf3-6a9313269975 stroke:#2c3143,stroke-width:4px;\n 19[\"Samtools view\"];\n 15 -->|bam_output| 19;\n 20[\"RmDup\"];\n 16 -->|outputsam| 20;\n 21[\"RmDup\"];\n 17 -->|outputsam| 21;\n 22[\"RmDup\"];\n 19 -->|outputsam| 22;\n 23[\"FreeBayes\"];\n 20 -->|output1| 23;\n 21 -->|output1| 23;\n 22 -->|output1| 23;\n 24[\"bcftools norm\"];\n 23 -->|output_vcf| 24;\n 25[\"SnpEff eff:\"];\n 24 -->|output_file| 25;\n 4aab5884-4099-4e41-a82d-c4e1ff19609f[\"Output\\nsnpeff_variant_stats\"];\n 25 --> 4aab5884-4099-4e41-a82d-c4e1ff19609f;\n style 4aab5884-4099-4e41-a82d-c4e1ff19609f stroke:#2c3143,stroke-width:4px;\n e5a2fbc7-acdd-4782-822a-91568cb8d5b8[\"Output\\nnormalized_snpeff_annotated_variants\"];\n 25 --> e5a2fbc7-acdd-4782-822a-91568cb8d5b8;\n style e5a2fbc7-acdd-4782-822a-91568cb8d5b8 stroke:#2c3143,stroke-width:4px;\n 26[\"GEMINI load\"];\n 25 -->|snpeff_output| 26;\n 6 -->|output| 26;\n 27[\"GEMINI inheritance pattern\"];\n 26 -->|outfile| 27;\n 07bd4bba-e7d9-48a8-b812-5dc2b07712bd[\"Output\\ncandidate_mutations\"];\n 27 --> 07bd4bba-e7d9-48a8-b812-5dc2b07712bd;\n style 07bd4bba-e7d9-48a8-b812-5dc2b07712bd stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Exome Seq Training Full W Cached Ref",
"outputs": [
{
@@ -877675,22 +816776,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n owner: galaxyp\n revisions: ae8c4b2488e7\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_merge\n owner: iuc\n revisions: 86296490704e\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n owner: iuc\n revisions: da6fc9f4a367\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ega_download_client\n owner: iuc\n revisions: 7d87a9d58aa1\n tool_panel_section_label: Get Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_inheritance\n owner: iuc\n revisions: 2c68e29c3527\n tool_panel_section_label: Gemini\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n owner: iuc\n revisions: 2270a8b83c12\n tool_panel_section_label: Gemini\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: geneiobio\n owner: iuc\n revisions: c0af7b196a89\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n owner: iuc\n revisions: 5c7b70713fb5\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json",
- "contributions": {
- "authorship": [
- "JasperO98",
- "wm75",
- "hexylena",
- "shiltemann"
- ],
- "reviewing": [
- "bgruening",
- "hexylena",
- "wm75",
- "JasperO98",
- "shiltemann",
- "lldelisle"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -877782,153 +816867,12 @@
"orcid": "0000-0003-3803-468X",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "by-covid",
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "nl",
- "email": "j.ouwerkerk.1@erasmusmc.nl",
- "id": "JasperO98",
- "joined": "2022-04",
- "name": "Jasper Ouwerkerk",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/JasperO98.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "ch",
- "email": "lucille.delisle@epfl.ch",
- "id": "lldelisle",
- "joined": "2019-08",
- "location": {
- "country": "CH",
- "lat": 46.52,
- "lon": 6.56
- },
- "name": "Lucille Delisle",
- "orcid": "0000-0002-1964-4960",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
}
],
"dir": "topics/variant-analysis/tutorials/trio-analysis",
"edam_operation": [
- "Genetic variation analysis",
- "Sequence analysis"
+ "Sequence analysis",
+ "Genetic variation analysis"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -877960,7 +816904,7 @@
"Pre-process VCFs using regular expressions.",
"Use annotations and phenotype information to find the causative variant(s)."
],
- "pageviews": 2877,
+ "pageviews": 2893,
"pub_date": "2022-05-19",
"questions": [
"How do you import data from the EGA?",
@@ -877983,18 +816927,18 @@
],
"short_id": "T00320",
"short_tools": [
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- "pyega3",
- "Filter1",
"bcftools_merge",
- "gemini_inheritance",
- "snpEff",
- "tp_grep_tool",
- "bcftools_norm",
- "gemini_load",
+ "Filter1",
"CONVERTER_gz_to_uncompressed",
"CONVERTER_uncompressed_to_gz",
- "gene_iobio_display_generation_iframe"
+ "snpEff",
+ "pyega3",
+ "regexColumn1",
+ "bcftools_norm",
+ "gene_iobio_display_generation_iframe",
+ "tp_grep_tool",
+ "gemini_inheritance",
+ "gemini_load"
],
"slides": false,
"slides_recordings": false,
@@ -878042,6 +816986,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -878097,10 +817045,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -878147,11 +817091,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -878196,6 +817135,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -878248,10 +817191,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -878292,10 +817231,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -878338,6 +817273,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -878390,10 +817329,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -878434,10 +817369,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -878480,6 +817411,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -878532,10 +817467,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -878576,10 +817507,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -878622,6 +817549,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -878676,10 +817607,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -878726,11 +817653,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -878777,171 +817699,12 @@
"state": "missing"
},
{
- "server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "missing"
- },
- {
- "server": "http://cropgalaxy.excellenceinbreeding.org/",
- "state": "missing"
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- {
- "server": "http://dintor.eurac.edu/",
- "state": "missing"
- },
- {
- "server": "http://www.freebioinfo.org/",
- "state": "missing"
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- {
- "server": "http://igg.cloud.ba.infn.it/galaxy",
- "state": "missing"
- },
- {
- "server": "https://galaxy.mesocentre.uca.fr",
- "state": "missing"
- },
- {
- "server": "https://galaxy.pasteur.fr/",
- "state": "inexact",
- "versions": [
- "1.0.3"
- ]
- },
- {
- "server": "https://galaxytrakr.org/",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "http://hyperbrowser.uio.no/hb/",
- "state": "missing"
- },
- {
- "server": "http://gigagalaxy.net/",
- "state": "missing"
- },
- {
- "server": "https://galaxy-web.ipk-gatersleben.de",
- "state": "missing"
- },
- {
- "server": "https://www.immportgalaxy.org/",
- "state": "missing"
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- {
- "server": "http://galaxy.interactomix.com/",
- "state": "missing"
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- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
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- {
- "server": "https://mississippi.sorbonne-universite.fr",
- "state": "inexact",
- "versions": [
- "1.0.3"
- ]
- },
- {
- "server": "https://neo.engr.uconn.edu/",
- "state": "missing"
- },
- {
- "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
- "state": "missing"
- },
- {
- "server": "http://galaxy.inf.ethz.ch",
- "state": "missing"
- },
- {
- "server": "https://palfinder.ls.manchester.ac.uk/",
- "state": "missing"
- },
- {
- "server": "http://pepsimili.e-nios.com:8080/",
- "state": "missing"
- },
- {
- "server": "https://galaxy.bio.di.uminho.pt/",
- "state": "missing"
- },
- {
- "server": "https://usegalaxy.be/",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.cz/",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
- "server": "https://usegalaxy.eu",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.no/",
- "state": "inexact",
- "versions": [
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- ]
- },
- {
- "server": "https://usegalaxy.org",
- "state": "exact",
- "version": "1.0.1"
- },
- {
- "server": "https://usegalaxy.org.au",
- "state": "exact",
- "version": "1.0.1"
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- {
- "server": "https://viralvariant.anses.fr/",
- "state": "missing"
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- "servers": [
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- "state": "missing"
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- {
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- "state": "missing"
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- "server": "https://vm-chemflow-francegrille.eu/",
- "state": "missing"
- },
- {
- "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
"state": "missing"
},
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
- "state": "inexact",
- "versions": [
- "1.4.0"
- ]
+ "state": "missing"
},
{
"server": "http://cropgalaxy.excellenceinbreeding.org/",
@@ -878967,13 +817730,13 @@
"server": "https://galaxy.pasteur.fr/",
"state": "inexact",
"versions": [
- "1.15.1+galaxy4"
+ "1.0.3"
]
},
{
"server": "https://galaxytrakr.org/",
"state": "exact",
- "version": "1.10"
+ "version": "1.0.1"
},
{
"server": "http://hyperbrowser.uio.no/hb/",
@@ -878996,7 +817759,161 @@
"state": "missing"
},
{
- "server": "http://galaxy.ul.edu.lb/",
+ "server": "https://mississippi.sorbonne-universite.fr",
+ "state": "inexact",
+ "versions": [
+ "1.0.3"
+ ]
+ },
+ {
+ "server": "https://neo.engr.uconn.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.inf.ethz.ch",
+ "state": "missing"
+ },
+ {
+ "server": "https://palfinder.ls.manchester.ac.uk/",
+ "state": "missing"
+ },
+ {
+ "server": "http://pepsimili.e-nios.com:8080/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.bio.di.uminho.pt/",
+ "state": "missing"
+ },
+ {
+ "server": "https://usegalaxy.be/",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.cz/",
+ "state": "inexact",
+ "versions": [
+ "1.0.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.eu",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.no/",
+ "state": "inexact",
+ "versions": [
+ "1.0.3"
+ ]
+ },
+ {
+ "server": "https://usegalaxy.org",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://usegalaxy.org.au",
+ "state": "exact",
+ "version": "1.0.1"
+ },
+ {
+ "server": "https://viralvariant.anses.fr/",
+ "state": "missing"
+ }
+ ],
+ "version": "1.0.1"
+ },
+ {
+ "id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+ "servers": [
+ {
+ "server": "http://apostl.moffitt.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://smile.hku.hk/SARGs",
+ "state": "missing"
+ },
+ {
+ "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+ "state": "missing"
+ },
+ {
+ "server": "https://vm-chemflow-francegrille.eu/",
+ "state": "missing"
+ },
+ {
+ "server": "https://hyperbrowser.uio.no/coloc-stats",
+ "state": "missing"
+ },
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://coralsnp.science.psu.edu/galaxy/",
+ "state": "inexact",
+ "versions": [
+ "1.4.0"
+ ]
+ },
+ {
+ "server": "http://cropgalaxy.excellenceinbreeding.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://dintor.eurac.edu/",
+ "state": "missing"
+ },
+ {
+ "server": "http://www.freebioinfo.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://igg.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.mesocentre.uca.fr",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy.pasteur.fr/",
+ "state": "inexact",
+ "versions": [
+ "1.15.1+galaxy4"
+ ]
+ },
+ {
+ "server": "https://galaxytrakr.org/",
+ "state": "exact",
+ "version": "1.10"
+ },
+ {
+ "server": "http://hyperbrowser.uio.no/hb/",
+ "state": "missing"
+ },
+ {
+ "server": "http://gigagalaxy.net/",
+ "state": "missing"
+ },
+ {
+ "server": "https://galaxy-web.ipk-gatersleben.de",
+ "state": "missing"
+ },
+ {
+ "server": "https://www.immportgalaxy.org/",
+ "state": "missing"
+ },
+ {
+ "server": "http://galaxy.interactomix.com/",
"state": "missing"
},
{
@@ -879044,11 +817961,6 @@
"state": "exact",
"version": "1.10"
},
- {
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- "state": "exact",
- "version": "1.10"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -879094,6 +818006,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879152,10 +818068,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -879201,11 +818113,6 @@
"state": "exact",
"version": "1.9+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -879225,8 +818132,8 @@
"1.9",
"1.4.0.0",
"1.15.1+galaxy3",
- "1.15.1+galaxy0",
- "1.15.1+galaxy2"
+ "1.15.1+galaxy2",
+ "1.15.1+galaxy0"
]
},
{
@@ -879259,6 +818166,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879311,10 +818222,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -879360,16 +818267,12 @@
"state": "exact",
"version": "5.0.2+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "4.0.0+galaxy0",
- "4.0.0+galaxy1"
+ "4.0.0+galaxy1",
+ "4.0.0+galaxy0"
]
},
{
@@ -879412,6 +818315,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879464,10 +818371,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -879511,11 +818414,6 @@
"state": "exact",
"version": "0.20.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -879561,6 +818459,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879613,10 +818515,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -879661,11 +818559,6 @@
"state": "exact",
"version": "0.20.1+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -879711,6 +818604,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879763,10 +818660,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -879811,10 +818704,6 @@
"state": "exact",
"version": "4.7.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -879860,6 +818749,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -879913,10 +818806,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -879961,11 +818850,6 @@
"state": "exact",
"version": "4.3+T.galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+T.galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -880030,7 +818914,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 239,
- "visitors": 1507,
+ "visitors": 1518,
"workflows": [
{
"creators": [
@@ -880235,7 +819119,7 @@
],
"license": "MIT",
"mermaid": "flowchart TD\n 0[\"EGA Download Client\"];\n 85672f3a-1556-49b6-be09-2e6c81721fb3[\"Output\\nEGA Download Client: authorized datasets\"];\n 0 --> 85672f3a-1556-49b6-be09-2e6c81721fb3;\n style 85672f3a-1556-49b6-be09-2e6c81721fb3 stroke:#2c3143,stroke-width:4px;\n 1[\"EGA Download Client\"];\n acd2bcf0-4b9d-4743-9034-716e73d4824f[\"Output\\nList of files in EGAD00001008392\"];\n 1 --> acd2bcf0-4b9d-4743-9034-716e73d4824f;\n style acd2bcf0-4b9d-4743-9034-716e73d4824f stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\npedigree\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Search in textfiles\"];\n 1 -->|dataset_file_list| 3;\n 6d5d135e-a373-4938-9374-019a09f45a51[\"Output\\nList of Case 5 VCFs\"];\n 3 --> 6d5d135e-a373-4938-9374-019a09f45a51;\n style 6d5d135e-a373-4938-9374-019a09f45a51 stroke:#2c3143,stroke-width:4px;\n 4[\"EGA Download Client\"];\n 3 -->|output| 4;\n bdce7169-390b-4adb-9305-5550d5d70a73[\"Output\\nCase 5 VCFs.gz\"];\n 4 --> bdce7169-390b-4adb-9305-5550d5d70a73;\n style bdce7169-390b-4adb-9305-5550d5d70a73 stroke:#2c3143,stroke-width:4px;\n 5[\"Convert compressed file to uncompressed.\"];\n 4 -->|downloaded_file_collection| 5;\n 82b71cdc-d813-4c77-8ff3-fa59e1725709[\"Output\\nCase 5 VCFs\"];\n 5 --> 82b71cdc-d813-4c77-8ff3-fa59e1725709;\n style 82b71cdc-d813-4c77-8ff3-fa59e1725709 stroke:#2c3143,stroke-width:4px;\n 6[\"Column Regex Find And Replace\"];\n 5 -->|output1| 6;\n 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27[\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"];\n 6 --> 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27;\n style 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27 stroke:#2c3143,stroke-width:4px;\n 7[\"bcftools norm\"];\n 6 -->|out_file1| 7;\n 96b34c8d-fa92-48cb-b01f-c05364deba5d[\"Output\\nCase 5 Normalized VCFs\"];\n 7 --> 96b34c8d-fa92-48cb-b01f-c05364deba5d;\n style 96b34c8d-fa92-48cb-b01f-c05364deba5d stroke:#2c3143,stroke-width:4px;\n 8[\"Filter\"];\n 7 -->|output_file| 8;\n a8539eb9-8bc3-473b-a27f-201c3acf5539[\"Output\\nCase 5 Normalized VCFs (Removed )\"];\n 8 --> a8539eb9-8bc3-473b-a27f-201c3acf5539;\n style a8539eb9-8bc3-473b-a27f-201c3acf5539 stroke:#2c3143,stroke-width:4px;\n 9[\"bcftools merge\"];\n 8 -->|out_file1| 9;\n b5c479b2-e58a-4fe2-b1cf-fc64476c8192[\"Output\\nCase 5 Merged VCF\"];\n 9 --> b5c479b2-e58a-4fe2-b1cf-fc64476c8192;\n style b5c479b2-e58a-4fe2-b1cf-fc64476c8192 stroke:#2c3143,stroke-width:4px;\n 10[\"SnpEff eff:\"];\n 9 -->|output_file| 10;\n cd7b4941-4f4c-4631-8ad5-3411e60fbbd9[\"Output\\nCase 5 SnpEff Annotated vcf\"];\n 10 --> cd7b4941-4f4c-4631-8ad5-3411e60fbbd9;\n style cd7b4941-4f4c-4631-8ad5-3411e60fbbd9 stroke:#2c3143,stroke-width:4px;\n 11[\"Convert uncompressed file to compressed\"];\n 10 -->|snpeff_output| 11;\n 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25[\"Output\\nSnpEff Annotated vcf_bgzip\"];\n 11 --> 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25;\n style 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25 stroke:#2c3143,stroke-width:4px;\n 12[\"gene.iobio visualisation\"];\n 11 -->|output1| 12;\n 11 -->|output1| 12;\n 11 -->|output1| 12;\n 0b30f4e0-7328-4479-8a56-bbf828fcfdba[\"Output\\nCase 5 gene.iobio results\"];\n 12 --> 0b30f4e0-7328-4479-8a56-bbf828fcfdba;\n style 0b30f4e0-7328-4479-8a56-bbf828fcfdba stroke:#2c3143,stroke-width:4px;\n 13[\"Case 5 GEMINI Database\"];\n 11 -->|output1| 13;\n 2 -->|output| 13;\n 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681[\"Output\\nGEMINI Database\"];\n 13 --> 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681;\n style 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681 stroke:#2c3143,stroke-width:4px;\n 14[\"Case 5 GEMINI Inheritance pattern\"];\n 13 -->|outfile| 14;\n 960ef978-089c-4292-81b5-731965c72a0d[\"Output\\nCase 5 GEMINI results\"];\n 14 --> 960ef978-089c-4292-81b5-731965c72a0d;\n style 960ef978-089c-4292-81b5-731965c72a0d stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:20 +0000",
"name": "Trio Analysis Tutorial",
"outputs": [
{
@@ -881232,15 +820116,15 @@
],
"dir": "topics/variant-analysis/tutorials/sars-cov-2",
"edam_operation": [
- "Data handling",
+ "Validation",
"Sequencing quality control",
"Formatting",
- "Sequence alignment",
- "Validation",
+ "Data handling",
"SNP detection",
- "Read mapping",
- "Generation",
"Sequence contamination filtering",
+ "Generation",
+ "Read mapping",
+ "Sequence alignment",
"Genome indexing"
],
"edam_topic": [],
@@ -881256,7 +820140,6 @@
"MISSISSIPPI",
"UseGalaxy.be",
"UseGalaxy.cz",
- "UseGalaxy.fr",
"UseGalaxy.no",
"UseGalaxy.org.au"
],
@@ -881278,7 +820161,7 @@
"Understand how collections enable processing of sequencing data in batches",
"Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
],
- "pageviews": 19146,
+ "pageviews": 19161,
"pub_date": "2020-06-24",
"questions": [
"How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -881301,20 +820184,20 @@
],
"short_id": "T00315",
"short_tools": [
- "picard_MarkDuplicates",
- "Grep1",
- "snpeff_sars_cov_2",
- "tp_cut_tool",
- "lofreq_viterbi",
+ "Filter1",
+ "fastp",
"lofreq_indelqual",
+ "lofreq_viterbi",
"lofreq_call",
+ "bwa_mem",
"multiqc",
- "Filter1",
- "snpSift_extractFields",
+ "Grep1",
+ "picard_MarkDuplicates",
+ "tp_cut_tool",
+ "snpeff_sars_cov_2",
"fasterq_dump",
- "fastp",
"samtools_stats",
- "bwa_mem"
+ "snpSift_extractFields"
],
"slides": false,
"slides_recordings": false,
@@ -881348,11 +820231,6 @@
"url": "https://usegalaxy.cz/",
"usegalaxy": false
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -881387,6 +820265,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -881442,10 +820324,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -881492,11 +820370,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -881541,6 +820414,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -881593,10 +820470,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -881637,10 +820510,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -881683,6 +820552,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -881735,10 +820608,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -881779,10 +820648,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -881825,6 +820690,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -881879,10 +820748,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -881930,11 +820795,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -881980,6 +820840,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882037,10 +820901,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882088,11 +820948,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882141,6 +820996,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882198,10 +821057,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882251,11 +821106,6 @@
"state": "exact",
"version": "2.18.2.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.18.2.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882301,6 +821151,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882361,10 +821215,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882413,11 +821263,6 @@
"state": "exact",
"version": "2.0.2+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882463,6 +821308,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882520,10 +821369,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882572,11 +821417,6 @@
"state": "exact",
"version": "0.20.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.20.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882625,6 +821465,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882680,10 +821524,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882732,11 +821572,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882782,6 +821617,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882834,10 +821673,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -882886,11 +821721,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -882936,6 +821766,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -882988,10 +821822,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -883036,11 +821866,6 @@
"state": "exact",
"version": "2.1.5+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.5+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -883086,6 +821911,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -883111,9 +821940,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -883150,10 +821979,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -883203,11 +822028,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -883253,6 +822073,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -883306,10 +822130,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -883354,11 +822174,6 @@
"state": "exact",
"version": "4.5covid19"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.5covid19"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -883404,6 +822219,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -883458,10 +822277,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -883506,11 +822321,6 @@
"state": "exact",
"version": "4.3+t.galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+t.galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -883556,6 +822366,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -883611,10 +822425,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -883661,28 +822471,6 @@
"state": "exact",
"version": "2.10.7+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "3.1.1+galaxy0",
- "2.10.4",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.8+galaxy0",
- "3.0.5+galaxy0",
- "2.10.7+galaxy2",
- "3.0.3+galaxy0",
- "2.11.0+galaxy1",
- "3.1.1+galaxy1",
- "3.0.8+galaxy0",
- "3.1.0+galaxy1",
- "3.0.10+galaxy0",
- "3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -883701,24 +822489,24 @@
"versions": [
"2.10.9+galaxy0",
"3.1.1+galaxy0",
+ "2.11.0+galaxy0",
"2.10.4",
"2.10.4+galaxy1",
- "2.11.0+galaxy0",
- "3.0.5+galaxy3",
- "2.10.4+galaxy2",
"2.10.8+galaxy0",
- "2.10.7+galaxy0",
+ "2.10.4+galaxy2",
"3.0.5+galaxy0",
+ "2.10.7+galaxy0",
"3.0.3+galaxy0",
+ "3.0.5+galaxy3",
+ "3.0.8+galaxy1",
"2.11.0+galaxy1",
"3.1.1+galaxy1",
"3.0.8+galaxy0",
"3.1.0+galaxy1",
- "3.0.10+galaxy0",
"3.1.0+galaxy0",
- "3.0.8+galaxy1",
- "3.0.0+galaxy0",
- "3.0.5+galaxy1"
+ "3.0.10+galaxy0",
+ "3.0.5+galaxy1",
+ "3.0.0+galaxy0"
]
},
{
@@ -883751,6 +822539,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -883806,10 +822598,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -883845,10 +822633,10 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.10.4",
- "2.10.4+galaxy1",
"2.10.7+galaxy1",
- "2.11.0+galaxy0"
+ "2.11.0+galaxy0",
+ "2.10.4",
+ "2.10.4+galaxy1"
]
},
{
@@ -883861,11 +822649,6 @@
"state": "exact",
"version": "3.0.3+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "3.0.3+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -883937,7 +822720,7 @@
"video_versions": 1,
"video_view": 0,
"visit_duration": 175,
- "visitors": 12595,
+ "visitors": 12606,
"workflows": [
{
"creators": [],
@@ -884068,7 +822851,7 @@
],
"license": null,
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"Faster Download and Extract Reads in FASTQ\"];\n 1 -->|output| 2;\n 3[\"fastp\"];\n 2 -->|list_paired| 3;\n 4[\"Map with BWA-MEM\"];\n 3 -->|output_paired_coll| 4;\n 0 -->|output| 4;\n 5[\"MarkDuplicates\"];\n 4 -->|bam_output| 5;\n 6[\"Realign reads\"];\n 5 -->|outFile| 6;\n 0 -->|output| 6;\n 7[\"Samtools stats\"];\n 5 -->|outFile| 7;\n 8[\"Insert indel qualities\"];\n 6 -->|realigned| 8;\n 0 -->|output| 8;\n 2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n 8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n 9[\"Call variants\"];\n 8 -->|output| 9;\n 0 -->|output| 9;\n 10[\"SnpEff eff:\"];\n 9 -->|variants| 10;\n 11[\"SnpSift Extract Fields\"];\n 10 -->|snpeff_output| 11;\n 06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n 11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n 12[\"MultiQC\"];\n 3 -->|report_json| 12;\n 7 -->|output| 12;\n 5 -->|metrics_file| 12;\n 10 -->|csvFile| 12;\n 758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n 12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Simple COVID-19 - PE Variation",
"outputs": [
{
@@ -884827,8 +823610,8 @@
"edam_operation": [
"Methylation analysis",
"Variant classification",
- "Tree-based sequence alignment",
- "Variant calling"
+ "Variant calling",
+ "Tree-based sequence alignment"
],
"edam_topic": [],
"exact_supported_servers": [
@@ -884863,7 +823646,7 @@
"Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
"Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
],
- "pageviews": 12244,
+ "pageviews": 12257,
"pub_date": "2021-06-30",
"questions": [
"How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -884926,12 +823709,12 @@
],
"short_id": "T00316",
"short_tools": [
+ "Filter1",
"datamash_ops",
- "pangolin",
"nextclade",
"fasta_regex_finder",
- "Filter1",
- "upload1"
+ "upload1",
+ "pangolin"
],
"slides": false,
"slides_recordings": false,
@@ -884979,6 +823762,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -885034,10 +823821,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -885084,11 +823867,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -885133,6 +823911,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -885185,10 +823967,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -885229,10 +824007,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -885275,6 +824049,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -885335,10 +824113,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -885386,11 +824160,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -885441,6 +824210,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -885494,10 +824267,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -885541,11 +824310,6 @@
"state": "exact",
"version": "2.7.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.7.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -885590,6 +824354,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -885622,11 +824390,11 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "4.1.2+galaxy0",
- "3.1.16+galaxy0",
"3.0.3+galaxy0",
+ "4.1.1+galaxy0",
"4.0.5+galaxy0",
- "4.1.1+galaxy0"
+ "3.1.16+galaxy0",
+ "4.1.2+galaxy0"
]
},
{
@@ -885649,10 +824417,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -885702,11 +824466,6 @@
"state": "exact",
"version": "4.3+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.3+galaxy2"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -885751,6 +824510,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -885803,10 +824566,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -885849,10 +824608,6 @@
"state": "exact",
"version": "0.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -885896,6 +824651,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -885948,10 +824707,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -885992,10 +824747,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -886052,8 +824803,8 @@
"video": true,
"video_versions": 3,
"video_view": 0,
- "visit_duration": 208,
- "visitors": 6643
+ "visit_duration": 209,
+ "visitors": 6653
},
{
"admin_install": {
@@ -886205,25 +824956,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: 86755160afbf\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: 86755160afbf\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n owner: devteam\n revisions: 63dd26468588\n tool_panel_section_label: EMBOSS\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 3d0c7bdf12f5\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 5ec9f6bceaee\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n owner: devteam\n revisions: 541082d03bef\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n owner: iuc\n revisions: da0bf365652d\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n owner: iuc\n revisions: c59d48774d03\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n owner: iuc\n revisions: a6e57ff585c0\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jvarkit_wgscoverageplotter\n owner: iuc\n revisions: ac048a34cac3\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n owner: iuc\n revisions: 20e2f64aa1fe\n tool_panel_section_label: Metagenomic Analysis\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mosdepth\n owner: iuc\n revisions: 5854d0da92b4\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n owner: iuc\n revisions: 4a89c6f84425\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n owner: iuc\n revisions: d220115f882b\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n owner: iuc\n revisions: 32f14a2723ec\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n owner: iuc\n revisions: 4839e590cb26\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n owner: iuc\n revisions: 42818629ec4c\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n owner: iuc\n revisions: 9793bc5d741b\n tool_panel_section_label: Annotation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
- "contributions": {
- "authorship": [
- "pvanheus",
- "slugger70",
- "thobalose"
- ],
- "reviewing": [
- "hexylena",
- "abueg",
- "wm75",
- "shiltemann",
- "gallardoalba",
- "bgruening",
- "bebatut",
- "pvanheus",
- "abretaud",
- "melpetera"
- ]
- },
"contributors": [
{
"bio": "Research at the South African National Bioinformatics Institute",
@@ -886252,206 +824984,6 @@
"name": "Thoba Lose",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/thobalose.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "id": "abueg",
- "joined": "2022-01",
- "name": "Linelle Abueg",
- "orcid": "0000-0002-6879-3954",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
- "twitter": "llabueg",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
- },
- {
- "affiliations": [
- "by-covid",
- "uni-freiburg",
- "elixir-europe"
- ],
- "elixir_node": "de",
- "fediverse": "https://scholar.social/@zerodivision",
- "fediverse_flavor": "mastodon",
- "id": "wm75",
- "joined": "2017-09",
- "matrix": "wm75:matrix.org",
- "name": "Wolfgang Maier",
- "orcid": "0000-0002-9464-6640",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "elixir_node": "de",
- "former_affiliations": [
- "uni-freiburg",
- "elixir-europe"
- ],
- "id": "gallardoalba",
- "joined": "2020-11",
- "name": "Crist\u00f3bal Gallardo",
- "orcid": "0000-0002-5752-2155",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "gallantries",
- "ifb",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "berenice.batut@gmail.com",
- "fediverse": "https://piaille.fr/@bebatut",
- "fediverse_flavor": "mastodon",
- "id": "bebatut",
- "joined": "2017-09",
- "linkedin": "berenicebatut",
- "location": {
- "country": "FR",
- "lat": 45.77,
- "lon": 3.08
- },
- "matrix": "bebatut:matrix.org",
- "name": "B\u00e9r\u00e9nice Batut",
- "orcid": "0000-0001-9852-1987",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
- "twitter": "bebatut",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
- },
- {
- "bio": "Research at the South African National Bioinformatics Institute",
- "id": "pvanheus",
- "joined": "2017-09",
- "name": "Peter van Heusden",
- "orcid": "0000-0001-6553-5274",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
- "twitter": "pvanheus",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
- },
- {
- "affiliations": [
- "gallantries",
- "eurosciencegateway",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "fr",
- "email": "anthony.bretaudeau@inrae.fr",
- "fediverse": "https://genomic.social/@abretaud",
- "fediverse_flavor": "mastodon",
- "id": "abretaud",
- "joined": "2017-09",
- "location": {
- "country": "FR",
- "lat": 48.11,
- "lon": -1.64
- },
- "matrix": "abretaud:matrix.org",
- "name": "Anthony Bretaudeau",
- "orcid": "0000-0003-0914-2470",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
- "twitter": "abretau",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
- },
- {
- "id": "melpetera",
- "joined": "2019-06",
- "name": "M\u00e9lanie Petera",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
}
],
"dir": "topics/variant-analysis/tutorials/tb-variant-analysis",
@@ -886464,22 +824996,22 @@
"topic_3324"
],
"edam_operation": [
- "Global alignment",
- "Variant calling",
+ "Validation",
+ "Phylogenetic tree generation",
"Statistical calculation",
"Sequencing quality control",
- "Phylogenetic tree generation",
- "Antimicrobial resistance prediction",
- "Sequence alignment analysis",
- "Sequence alignment",
- "Taxonomic classification",
- "Validation",
+ "Local alignment",
+ "Sequence composition calculation",
"Phylogenetic tree visualisation",
+ "Taxonomic classification",
+ "Sequence contamination filtering",
+ "Sequence alignment analysis",
+ "Variant calling",
+ "Antimicrobial resistance prediction",
"Sequence analysis",
- "Sequence composition calculation",
+ "Sequence alignment",
"Genome visualisation",
- "Sequence contamination filtering",
- "Local alignment"
+ "Global alignment"
],
"edam_topic": [
"Genomics",
@@ -886514,7 +825046,7 @@
"How can we predict drug resistance from those variants",
"How do we annotate those variants"
],
- "pageviews": 9478,
+ "pageviews": 9516,
"pub_date": "2020-07-25",
"questions": [
"How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
@@ -886549,26 +825081,26 @@
],
"short_id": "T00319",
"short_tools": [
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- "tp_awk_tool",
- "jbrowse",
- "upload1",
"fastp",
"multiqc",
- "snippy",
- "tp_sed_tool",
- "kraken2",
- "bcftools_consensus",
- "qualimap_bamqc",
"tbvcfreport",
- "__FLATTEN__",
- "jvarkit_wgscoverageplotter",
+ "qualimap_bamqc",
"EMBOSS:%20seqret84",
- "tb_variant_filter",
- "fastqc",
"tb_profiler_profile",
- "samtools_stats",
- "EMBOSS: seqret84"
+ "jvarkit_wgscoverageplotter",
+ "mosdepth",
+ "EMBOSS: seqret84",
+ "__FLATTEN__",
+ "fastqc",
+ "jbrowse",
+ "tb_variant_filter",
+ "tp_sed_tool",
+ "kraken2",
+ "snippy",
+ "bcftools_consensus",
+ "tp_awk_tool",
+ "upload1",
+ "samtools_stats"
],
"slides": false,
"slides_recordings": false,
@@ -886599,6 +825131,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -886654,10 +825190,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -886704,11 +825236,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -886753,6 +825280,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -886805,10 +825336,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -886849,10 +825376,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -886895,6 +825418,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -886954,10 +825481,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -887010,11 +825533,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -887064,6 +825582,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887118,10 +825640,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -887168,11 +825686,6 @@
"state": "exact",
"version": "1.1.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -887218,6 +825731,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887276,10 +825793,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -887331,11 +825844,6 @@
"state": "exact",
"version": "9.3+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "9.3+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -887384,6 +825892,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887437,10 +825949,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -887485,11 +825993,6 @@
"state": "exact",
"version": "5.0.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "5.0.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -887535,6 +826038,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887587,10 +826094,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -887631,10 +826134,6 @@
"server": "https://usegalaxy.eu",
"state": "missing"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -887677,6 +826176,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887734,10 +826237,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -887763,8 +826262,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -887788,12 +826287,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -887803,9 +826302,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -887816,11 +826315,6 @@
"state": "exact",
"version": "0.73+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.73+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -887866,6 +826360,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -887891,8 +826389,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -887929,10 +826427,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -887956,8 +826450,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -887977,12 +826471,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -887995,11 +826489,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -888048,6 +826537,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -888108,10 +826601,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -888147,8 +826636,8 @@
"versions": [
"2.0.2+galaxy2",
"2.0",
- "2.0.1",
"2.0.2",
+ "2.0.1",
"2.0.2+galaxy1"
]
},
@@ -888164,11 +826653,6 @@
"state": "exact",
"version": "2.0.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.5"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -888218,6 +826702,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -888274,10 +826762,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -888312,10 +826796,10 @@
"state": "inexact",
"versions": [
"1.9+galaxy2",
- "1.9+galaxy1",
- "1.10",
+ "1.9",
"1.4.0",
- "1.9"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -888328,18 +826812,13 @@
"state": "exact",
"version": "1.15.1+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
"1.10+galaxy1",
- "1.9+galaxy1",
- "1.10"
+ "1.10",
+ "1.9+galaxy1"
]
},
{
@@ -888382,6 +826861,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -888446,10 +826929,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -888485,11 +826964,11 @@
"versions": [
"0.20.1+galaxy0",
"0.19.5+galaxy1",
- "0.19.3.3",
- "0.18.0.0",
- "0.12.4.0",
"0.19.3.2",
- "0.19.5"
+ "0.12.4.0",
+ "0.19.5",
+ "0.18.0.0",
+ "0.19.3.3"
]
},
{
@@ -888504,11 +826983,6 @@
"state": "exact",
"version": "0.23.4+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.23.4+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -888525,9 +826999,9 @@
"0.20.1+galaxy0",
"0.19.5+galaxy1",
"0.23.2+galaxy0",
+ "0.24.0+galaxy3",
"0.23.4+galaxy2",
- "0.23.4+galaxy1",
- "0.24.0+galaxy3"
+ "0.23.4+galaxy1"
]
},
{
@@ -888568,6 +827042,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -888623,10 +827101,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -888662,23 +827136,23 @@
"versions": [
"1.16.9+galaxy0",
"1.16.10+galaxy0",
- "1.12.5+galaxy2",
+ "0.7.0.3",
+ "1.16.5+galaxy7",
+ "0.1",
"1.16.4+galaxy2",
+ "0.5.2.1",
+ "1.12.5+galaxy1",
+ "1.12.5+galaxy2",
+ "1.16.4+galaxy3",
"1.16.1+galaxy0",
"1.16.5+galaxy5",
+ "1.12.5+galaxy0",
"1.16.5+galaxy3",
- "1.12.5+galaxy1",
- "1.16.5+galaxy4",
- "0.5.2.1",
- "1.16.4+galaxy3",
- "1.16.8+galaxy1",
- "1.16.5+galaxy7",
"1.12.5+galaxy3",
- "1.12.5+galaxy0",
- "0.7.0.3",
+ "1.16.8+galaxy1",
"1.16.8+galaxy0",
- "1.16.5+galaxy6",
- "0.1"
+ "1.16.5+galaxy4",
+ "1.16.5+galaxy6"
]
},
{
@@ -888691,11 +827165,6 @@
"state": "exact",
"version": "1.16.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.16.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -888741,6 +827210,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -888793,10 +827266,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
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@@ -888839,10 +827308,6 @@
"state": "exact",
"version": "20201223+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -888886,6 +827351,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
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+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -888940,10 +827409,6 @@
"server": "http://galaxy.interactomix.com/",
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},
- {
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -888977,8 +827442,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.0.7_beta+galaxy0",
- "2.0.8_beta+galaxy0"
+ "2.0.8_beta+galaxy0",
+ "2.0.7_beta+galaxy0"
]
},
{
@@ -888991,11 +827456,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.1.1+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -889041,6 +827501,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -889096,10 +827560,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -889145,10 +827605,6 @@
"state": "exact",
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},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
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{
"server": "https://usegalaxy.no/",
"state": "missing"
@@ -889193,6 +827649,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -889247,10 +827707,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -889299,11 +827755,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -889314,8 +827765,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -889358,6 +827809,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
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@@ -889416,10 +827871,6 @@
"server": "http://galaxy.interactomix.com/",
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{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -889466,14 +827917,6 @@
"state": "exact",
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},
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- "state": "inexact",
- "versions": [
- "2.3+galaxy0",
- "2.2.2d+galaxy3"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -889529,6 +827972,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -889582,10 +828029,6 @@
"server": "http://galaxy.interactomix.com/",
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- {
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- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -889619,14 +828062,14 @@
"state": "inexact",
"versions": [
"4.5.0",
- "3.2+galaxy1",
- "4.4.5+galaxy0",
- "4.4.3+galaxy0",
"3.2",
- "4.3.6+galaxy2",
- "4.4.5+galaxy2",
"4.4.5+galaxy1",
- "4.3.6+galaxy1"
+ "4.3.6+galaxy1",
+ "4.4.3+galaxy0",
+ "3.2+galaxy1",
+ "4.3.6+galaxy2",
+ "4.4.5+galaxy0",
+ "4.4.5+galaxy2"
]
},
{
@@ -889639,17 +828082,12 @@
"state": "exact",
"version": "4.6.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "4.6.0+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "3.2+galaxy1",
- "3.2"
+ "3.2",
+ "3.2+galaxy1"
]
},
{
@@ -889692,6 +828130,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -889744,10 +828186,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -889793,10 +828231,6 @@
"state": "exact",
"version": "0.4.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -889846,6 +828280,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -889898,10 +828336,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -889934,13 +828368,13 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "2.8.14+galaxy1",
+ "2.4",
+ "2.8.3+galaxy0",
"2.8.4+galaxy1",
+ "2.1.0",
"2.6.1+galaxy0",
- "2.8.3+galaxy0",
"2.6+galaxy0",
- "2.1.0",
- "2.4"
+ "2.8.14+galaxy1"
]
},
{
@@ -889955,22 +828389,18 @@
"state": "exact",
"version": "6.2.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
"versions": [
- "2.8.14+galaxy1",
"2.8.4+galaxy1",
- "4.1.1+galaxy0",
+ "2.8.14+galaxy1",
"3.0.6+galaxy0",
- "3.0.8+galaxy0",
- "3.0.7+galaxy1",
+ "3.0.4+galaxy1",
"3.0.7+galaxy0",
- "3.0.4+galaxy1"
+ "4.1.1+galaxy0",
+ "3.0.7+galaxy1",
+ "3.0.8+galaxy0"
]
},
{
@@ -890013,6 +828443,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -890065,10 +828499,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -890116,10 +828546,6 @@
"state": "exact",
"version": "1.0.0+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -890169,6 +828595,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -890221,10 +828651,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -890272,10 +828698,6 @@
"state": "exact",
"version": "1.0.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -890325,6 +828747,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -890377,10 +828803,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -890421,10 +828843,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -890499,8 +828917,8 @@
"video": true,
"video_versions": 2,
"video_view": 0,
- "visit_duration": 175,
- "visitors": 6039,
+ "visit_duration": 174,
+ "visitors": 6071,
"workflows": [
{
"creators": [
@@ -890759,7 +829177,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Collection\\nReads\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n style 2 fill:#ded,stroke:#393,stroke-width:4px;\n 3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n style 3 fill:#ded,stroke:#393,stroke-width:4px;\n 4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n style 4 fill:#ded,stroke:#393,stroke-width:4px;\n 5[\"fastp\"];\n 0 -->|output| 5;\n 6[\"seqret\"];\n 1 -->|output| 6;\n 7[\"snippy\"];\n 4 -->|output| 7;\n 2 -->|output| 7;\n 3 -->|output| 7;\n 5 -->|output_paired_coll| 7;\n 1 -->|output| 7;\n 8[\"Kraken2\"];\n 5 -->|output_paired_coll| 8;\n c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n 8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n 083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n 8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n 9[\"QualiMap BamQC\"];\n 7 -->|snpsbam| 9;\n 10[\"mosdepth\"];\n 2 -->|output| 10;\n 7 -->|snpsbam| 10;\n 11[\"TB Variant Filter\"];\n 7 -->|snpvcf| 11;\n 12[\"TB-Profiler Profile\"];\n 7 -->|snpsbam| 12;\n 335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n 12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n 13[\"TB Variant Filter\"];\n 7 -->|snpvcf| 13;\n 14[\"Flatten collection\"];\n 9 -->|raw_data| 14;\n 15[\"Text reformatting\"];\n 10 -->|output_quantized_bed| 15;\n 16[\"Text transformation\"];\n 11 -->|output1| 16;\n 007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n 16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n 17[\"MultiQC\"];\n 5 -->|report_json| 17;\n 14 -->|output| 17;\n 59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n 17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n 18[\"bcftools consensus\"];\n 13 -->|output1| 18;\n 6 -->|out_file1| 18;\n 15 -->|outfile| 18;\n c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n 18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n 19[\"TB Variant Report\"];\n 16 -->|output| 19;\n 12 -->|results_json| 19;\n 959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n 19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n 19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:20 +0000",
"name": "TB Variant Analysis v1.0",
"outputs": [
{
@@ -891387,23 +829805,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n owner: bgruening\n revisions: d698c222f354\n tool_panel_section_label: Text Manipulation\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n owner: devteam\n revisions: 3fe632431b68\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n owner: devteam\n revisions: e188dc7a68e6\n tool_panel_section_label: Mapping\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: e7b2202befea\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n owner: devteam\n revisions: 5ec9f6bceaee\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n owner: devteam\n revisions: 57def2d7c093\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n owner: devteam\n revisions: a5937157062f\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_calmd\n owner: devteam\n revisions: 06dc50b7b711\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_calmd\n owner: devteam\n revisions: 92ec40abcdcf\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_rmdup\n owner: devteam\n revisions: 586f9e1cdb2b\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n owner: iuc\n revisions: df7356989ac1\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n owner: iuc\n revisions: 31a35811dda6\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: control_freec\n owner: iuc\n revisions: 2c6349fb175c\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: control_freec\n owner: iuc\n revisions: f923c54a17ee\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: abfd8a6544d7\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n owner: iuc\n revisions: bf675f34b056\n tool_panel_section_label: Quality Control\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n owner: iuc\n revisions: 5826298f6a73\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n owner: iuc\n revisions: b72793637686\n tool_panel_section_label: SAM/BAM\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n owner: pjbriggs\n revisions: dfa082f84068\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n owner: pjbriggs\n revisions: 32f1f56bd970\n tool_panel_section_label: FASTA/FASTQ\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.json",
- "contributions": {
- "authorship": [
- "khaled196",
- "kkamieniecka",
- "wm75",
- "d-salgado",
- "poterlowicz-lab"
- ],
- "reviewing": [
- "shiltemann",
- "hexylena",
- "khaled196",
- "slugger70",
- "bgruening",
- "kkamieniecka"
- ]
- },
"contributors": [
{
"affiliations": [
@@ -891467,152 +829868,22 @@
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
"twitter": "bioinfbrad",
"url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
- },
- {
- "affiliations": [
- "uni-freiburg",
- "nfdi4plants",
- "elixir-europe"
- ],
- "bio": "Researcher at Erasmus Medical Center",
- "bluesky": "shiltemann.bsky.social",
- "contact_for_training": true,
- "elixir_node": "nl",
- "email": "saskia.hiltemann@gmail.com",
- "fediverse": "https://mstdn.science/@shiltemann",
- "fediverse_flavor": "mastodon",
- "former_affiliations": [
- "CINECA-Project",
- "gallantries",
- "erasmusmc"
- ],
- "id": "shiltemann",
- "joined": "2017-09",
- "linkedin": "shiltemann",
- "location": {
- "country": "NL",
- "lat": 51.912,
- "lon": 4.462
- },
- "maintainer_contact": "gitter",
- "matrix": "shiltemann:matrix.org",
- "name": "Saskia Hiltemann",
- "orcid": "0000-0003-3803-468X",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
- },
- {
- "affiliations": [
- "erasmusmc",
- "gallantries",
- "by-covid",
- "elixir-europe",
- "elixir-converge"
- ],
- "contact_for_training": false,
- "elixir_node": "nl",
- "former_affiliations": [
- "deNBI",
- "avans-atgm",
- "uni-freiburg"
- ],
- "id": "hexylena",
- "joined": "2017-09",
- "location": {
- "country": "NL",
- "lat": 51.91,
- "lon": 4.46
- },
- "maintainer_contact": "gitter",
- "matrix": "hexylena:matrix.org",
- "name": "Helena Rasche",
- "orcid": "0000-0001-9760-8992",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "email": "k.jumah@bradford.ac.uk",
- "id": "khaled196",
- "joined": "2022-09",
- "name": "Khaled Jum\u2019ah",
- "orcid": "0000-0001-5481-8893",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
- },
- {
- "elixir_node": "au",
- "email": "simon.gladman@unimelb.edu.au",
- "id": "slugger70",
- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend. He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
- "joined": "2017-09",
- "name": "Simon Gladman",
- "orcid": "0000-0002-6100-4385",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
- },
- {
- "affiliations": [
- "eurosciencegateway",
- "eosc-life",
- "by-covid",
- "deNBI",
- "sfb992",
- "elixir-converge",
- "uni-freiburg",
- "elixir-europe"
- ],
- "contact_for_training": true,
- "elixir_node": "de",
- "email": "bjoern.gruening@gmail.com",
- "fediverse": "https://fosstodon.org/@bgruening",
- "fediverse_flavor": "mastodon",
- "id": "bgruening",
- "joined": "2017-09",
- "linkedin": "bgruening",
- "location": {
- "country": "DE",
- "lat": 47.997791,
- "lon": 7.842609
- },
- "matrix": "bgruening:matrix.org",
- "name": "Bj\u00f6rn Gr\u00fcning",
- "orcid": "0000-0002-3079-6586",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
- "twitter": "bjoerngruening",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
- },
- {
- "affiliations": [
- "elixir-europe"
- ],
- "elixir_node": "uk",
- "id": "kkamieniecka",
- "joined": "2018-08",
- "name": "Katarzyna Kamieniecka",
- "orcid": "0009-0004-2454-5950",
- "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
- "twitter": "katemurat",
- "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
}
],
"dir": "topics/variant-analysis/tutorials/somatic-variant-discovery",
"edam_operation": [
- "Sequence visualisation",
- "Variant calling",
+ "Validation",
+ "Sequence alignment",
+ "Copy number estimation",
"Statistical calculation",
"Sequencing quality control",
- "Copy number estimation",
- "Sequence alignment",
- "Validation",
"Sequence composition calculation",
+ "Sequence visualisation",
+ "Variant calling",
+ "Genome alignment",
"Read mapping",
"Generation",
- "Genome indexing",
- "Genome alignment"
+ "Genome indexing"
],
"edam_topic": [],
"exact_supported_servers": [],
@@ -891641,7 +829912,7 @@
"Use Control-Freec for hCNV Identefication in tumor tissue.",
"Visualise the detected hCNVs in specific chromosomes."
],
- "pageviews": 1722,
+ "pageviews": 1733,
"pub_date": "2022-10-05",
"questions": [
"What are the specific challenges in locating human Copy Number Variances (hCNVs)?",
@@ -891651,22 +829922,22 @@
],
"short_id": "T00317",
"short_tools": [
- "Grep1",
- "tp_text_file_with_recurring_lines",
- "circos",
- "fastqc",
+ "samtools_rmdup",
"control_freec",
- "samtools_calmd",
+ "__RELABEL_FROM_FILE__",
"__BUILD_LIST__",
+ "tp_text_file_with_recurring_lines",
+ "bamleftalign",
+ "bwa_mem",
+ "fastqc",
"multiqc",
- "tp_replace_in_line",
- "__RELABEL_FROM_FILE__",
+ "samtools_view",
+ "Grep1",
"__EXTRACT_DATASET__",
- "bamleftalign",
- "samtools_rmdup",
"trimmomatic",
- "bwa_mem",
- "samtools_view"
+ "tp_replace_in_line",
+ "samtools_calmd",
+ "circos"
],
"slides": false,
"slides_recordings": false,
@@ -891723,6 +829994,10 @@
"name": "Coloc-stats",
"url": "https://hyperbrowser.uio.no/coloc-stats"
},
+ {
+ "name": "CorGAT",
+ "url": "http://corgat.cloud.ba.infn.it/galaxy"
+ },
{
"name": "CoralSNP",
"url": "https://coralsnp.science.psu.edu/galaxy/"
@@ -891778,10 +830053,6 @@
"name": "InteractoMIX",
"url": "http://galaxy.interactomix.com/"
},
- {
- "name": "Lebanese University Galaxy",
- "url": "http://galaxy.ul.edu.lb/"
- },
{
"name": "MISSISSIPPI",
"url": "https://mississippi.sorbonne-universite.fr",
@@ -891828,11 +830099,6 @@
"url": "https://usegalaxy.eu",
"usegalaxy": true
},
- {
- "name": "UseGalaxy.fr",
- "url": "https://usegalaxy.fr/",
- "usegalaxy": false
- },
{
"name": "UseGalaxy.no",
"url": "https://usegalaxy.no/",
@@ -891877,6 +830143,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "local"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -891929,10 +830199,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -891973,10 +830239,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -892019,6 +830281,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892071,10 +830337,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -892115,10 +830377,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -892161,6 +830419,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892213,10 +830475,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -892257,10 +830515,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -892303,6 +830557,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "local"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "local"
@@ -892355,10 +830613,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "local"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "local"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "local"
@@ -892399,10 +830653,6 @@
"server": "https://usegalaxy.eu",
"state": "local"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "local"
- },
{
"server": "https://usegalaxy.no/",
"state": "local"
@@ -892445,6 +830695,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892499,10 +830753,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -892549,11 +830799,6 @@
"state": "exact",
"version": "1.1.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -892599,6 +830844,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892653,10 +830902,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -892703,11 +830948,6 @@
"state": "exact",
"version": "1.1.0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.1.0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -892753,6 +830993,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892810,10 +831054,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -892861,11 +831101,6 @@
"state": "exact",
"version": "0.7.17.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -892914,6 +831149,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -892973,10 +831212,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -893024,11 +831259,6 @@
"state": "exact",
"version": "0.7.17.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.7.17.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -893075,6 +831305,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893132,10 +831366,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -893186,9 +831416,9 @@
"0.74+galaxy0",
"0.69",
"0.65",
- "0.67",
"0.68",
"0.52",
+ "0.67",
"0.63",
"0.64",
"0.62"
@@ -893199,11 +831429,6 @@
"state": "exact",
"version": "0.72+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.72+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -893249,6 +831474,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893274,8 +831503,8 @@
"state": "inexact",
"versions": [
"0.72+galaxy1",
- "0.73+galaxy0",
- "0.72"
+ "0.72",
+ "0.73+galaxy0"
]
},
{
@@ -893312,10 +831541,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -893339,8 +831564,8 @@
"versions": [
"0.72+galaxy1",
"0.72",
- "0.65",
- "0.71"
+ "0.71",
+ "0.65"
]
},
{
@@ -893360,12 +831585,12 @@
"0.72+galaxy1",
"0.72",
"0.69",
- "0.65",
"0.71",
- "0.67",
+ "0.65",
"0.68",
+ "0.74+galaxy1",
"0.52",
- "0.74+galaxy1"
+ "0.67"
]
},
{
@@ -893378,11 +831603,6 @@
"state": "exact",
"version": "0.74+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.74+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -893431,6 +831651,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893487,10 +831711,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -893539,11 +831759,6 @@
"state": "exact",
"version": "1.3.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -893589,6 +831804,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893645,10 +831864,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -893683,8 +831898,8 @@
"state": "inexact",
"versions": [
"1.3.1",
- "1.1.0.46-0",
- "1.0.2.29"
+ "1.0.2.29",
+ "1.1.0.46-0"
]
},
{
@@ -893697,11 +831912,6 @@
"state": "exact",
"version": "1.3.6"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.3.6"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -893747,6 +831957,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893800,10 +832014,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -893849,11 +832059,6 @@
"state": "exact",
"version": "2.0.2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.2"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -893899,6 +832104,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -893955,10 +832164,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -894006,11 +832211,6 @@
"state": "exact",
"version": "2.0.3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894056,6 +832256,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894109,10 +832313,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -894157,11 +832357,6 @@
"state": "exact",
"version": "2.0.1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "2.0.1"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894207,6 +832402,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894263,10 +832462,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -894319,11 +832514,6 @@
"0.69.8+galaxy10"
]
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.69.8+galaxy7"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894369,6 +832559,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894429,10 +832623,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -894470,9 +832660,9 @@
"versions": [
"0.69.8+galaxy7",
"0.69.8+galaxy4",
- "0.69.8+galaxy1",
"0.69.8+galaxy2",
- "0.69.8+galaxy3"
+ "0.69.8+galaxy3",
+ "0.69.8+galaxy1"
]
},
{
@@ -894485,11 +832675,6 @@
"state": "exact",
"version": "0.69.8+galaxy9"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.69.8+galaxy9"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894502,8 +832687,8 @@
"0.69.8+galaxy12",
"0.69.8+galaxy7",
"0.69.8+galaxy4",
- "0.69.8+galaxy1",
"0.69.8+galaxy2",
+ "0.69.8+galaxy1",
"0.69.8+galaxy10"
]
},
@@ -894551,6 +832736,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894603,10 +832792,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -894652,10 +832837,6 @@
"state": "exact",
"version": "11.6+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894702,6 +832883,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894754,10 +832939,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "missing"
@@ -894803,10 +832984,6 @@
"state": "exact",
"version": "11.6+galaxy2"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "missing"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -894851,6 +833028,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -894905,10 +833086,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "exact",
@@ -894957,11 +833134,6 @@
"state": "exact",
"version": "1.11+galaxy1"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.11+galaxy1"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -894972,8 +833144,8 @@
"1.9",
"1.8+galaxy0",
"1.8+galaxy2",
- "1.7.1",
- "1.8+galaxy1"
+ "1.8+galaxy1",
+ "1.7.1"
]
},
{
@@ -895016,6 +833188,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -895041,9 +833217,9 @@
"state": "inexact",
"versions": [
"1.11+galaxy1",
+ "1.6",
"1.11+galaxy0",
- "1.7",
- "1.6"
+ "1.7"
]
},
{
@@ -895080,10 +833256,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -895133,11 +833305,6 @@
"state": "exact",
"version": "1.8+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.8+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -895183,6 +833350,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -895207,8 +833378,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -895242,10 +833413,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -895295,11 +833462,6 @@
"state": "exact",
"version": "1.15.1+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.15.1+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -895345,6 +833507,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -895369,8 +833535,8 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
- "1.15.1+galaxy2",
- "1.9"
+ "1.9",
+ "1.15.1+galaxy2"
]
},
{
@@ -895402,10 +833568,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -895457,11 +833619,6 @@
"state": "exact",
"version": "1.9+galaxy3"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "1.9+galaxy3"
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -895507,6 +833664,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -895531,10 +833692,10 @@
"server": "https://galaxy.mesocentre.uca.fr",
"state": "inexact",
"versions": [
+ "0.36.6",
"0.38.0",
- "0.38.1",
"0.39+galaxy0",
- "0.36.6"
+ "0.38.1"
]
},
{
@@ -895545,8 +833706,8 @@
"server": "https://galaxytrakr.org/",
"state": "inexact",
"versions": [
- "0.38.1",
"0.39+galaxy0",
+ "0.38.1",
"0.36.4"
]
},
@@ -895570,10 +833731,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -895621,9 +833778,9 @@
"0.38.1",
"0.36.4",
"0.32.3",
+ "0.36.0",
"0.32.1",
- "0.32.2",
- "0.36.0"
+ "0.32.2"
]
},
{
@@ -895631,17 +833788,6 @@
"state": "exact",
"version": "0.36.5"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "inexact",
- "versions": [
- "0.38.0",
- "0.38.1",
- "0.39+galaxy0",
- "0.39+galaxy2",
- "0.39+galaxy1"
- ]
- },
{
"server": "https://usegalaxy.no/",
"state": "exact",
@@ -895687,6 +833833,10 @@
"server": "https://hyperbrowser.uio.no/coloc-stats",
"state": "missing"
},
+ {
+ "server": "http://corgat.cloud.ba.infn.it/galaxy",
+ "state": "missing"
+ },
{
"server": "https://coralsnp.science.psu.edu/galaxy/",
"state": "missing"
@@ -895741,10 +833891,6 @@
"server": "http://galaxy.interactomix.com/",
"state": "missing"
},
- {
- "server": "http://galaxy.ul.edu.lb/",
- "state": "missing"
- },
{
"server": "https://mississippi.sorbonne-universite.fr",
"state": "inexact",
@@ -895768,9 +833914,9 @@
"server": "https://palfinder.ls.manchester.ac.uk/",
"state": "inexact",
"versions": [
+ "0.36.6",
"0.38.0",
"0.38.1",
- "0.36.6",
"0.36.4",
"0.36.5",
"0.32.3"
@@ -895791,8 +833937,8 @@
"server": "https://usegalaxy.be/",
"state": "inexact",
"versions": [
- "0.38.0",
"0.36.6",
+ "0.38.0",
"0.39+galaxy2",
"0.36.5",
"0.32.3"
@@ -895805,9 +833951,9 @@
"0.38.1",
"0.36.4",
"0.32.3",
+ "0.36.0",
"0.32.1",
- "0.32.2",
- "0.36.0"
+ "0.32.2"
]
},
{
@@ -895815,11 +833961,6 @@
"state": "exact",
"version": "0.39+galaxy0"
},
- {
- "server": "https://usegalaxy.fr/",
- "state": "exact",
- "version": "0.39+galaxy0"
- },
{
"server": "https://usegalaxy.no/",
"state": "inexact",
@@ -895833,9 +833974,9 @@
"server": "https://usegalaxy.org",
"state": "inexact",
"versions": [
+ "0.36.6",
"0.38.0",
"0.38.1",
- "0.36.6",
"0.39+galaxy2",
"0.36.5",
"0.32.3",
@@ -895910,7 +834051,7 @@
"video_versions": 0,
"video_view": 0,
"visit_duration": 114,
- "visitors": 1318,
+ "visitors": 1325,
"workflows": [
{
"creators": [
@@ -896100,7 +834241,7 @@
],
"license": "AGPL-3.0-or-later",
"mermaid": "flowchart TD\n 0[\"\u2139\ufe0f Input Dataset\\nNormal_r1.fastq.gz\"];\n style 0 stroke:#2c3143,stroke-width:4px;\n 1[\"\u2139\ufe0f Input Dataset\\nNormal_r2.fastq.gz\"];\n style 1 stroke:#2c3143,stroke-width:4px;\n 2[\"\u2139\ufe0f Input Dataset\\nTumor_r1.fastq.gz\"];\n style 2 stroke:#2c3143,stroke-width:4px;\n 3[\"Create text file\"];\n 4[\"\u2139\ufe0f Input Dataset\\nTumor_r2.fastq.gz\"];\n style 4 stroke:#2c3143,stroke-width:4px;\n 5[\"\u2139\ufe0f Input Dataset\\ncapture_targets_chr5_12_17.bed\"];\n style 5 stroke:#2c3143,stroke-width:4px;\n 6[\"FastQC\"];\n 0 -->|output| 6;\n 7[\"Trimmomatic\"];\n 0 -->|output| 7;\n 1 -->|output| 7;\n 8[\"FastQC\"];\n 1 -->|output| 8;\n 9[\"FastQC\"];\n 2 -->|output| 9;\n 10[\"Trimmomatic\"];\n 2 -->|output| 10;\n 4 -->|output| 10;\n 11[\"FastQC\"];\n 4 -->|output| 11;\n 12[\"FastQC\"];\n 7 -->|fastq_out_r2_paired| 12;\n 13[\"Map with BWA-MEM\"];\n 7 -->|fastq_out_r1_paired| 13;\n 7 -->|fastq_out_r2_paired| 13;\n 14[\"FastQC\"];\n 7 -->|fastq_out_r1_paired| 14;\n 15[\"FastQC\"];\n 10 -->|fastq_out_r2_paired| 15;\n 16[\"Map with BWA-MEM\"];\n 10 -->|fastq_out_r1_paired| 16;\n 10 -->|fastq_out_r2_paired| 16;\n 17[\"FastQC\"];\n 10 -->|fastq_out_r1_paired| 17;\n 18[\"MultiQC\"];\n 9 -->|text_file| 18;\n 6 -->|text_file| 18;\n 8 -->|text_file| 18;\n 11 -->|text_file| 18;\n 19[\"Build list\"];\n 13 -->|bam_output| 19;\n 16 -->|bam_output| 19;\n 20[\"MultiQC\"];\n 12 -->|text_file| 20;\n 14 -->|text_file| 20;\n 15 -->|text_file| 20;\n 17 -->|text_file| 20;\n 21[\"Relabel identifiers\"];\n 3 -->|outfile| 21;\n 19 -->|output| 21;\n 22[\"Samtools view\"];\n 21 -->|output| 22;\n 23[\"RmDup\"];\n 22 -->|outputsam| 23;\n 24[\"BamLeftAlign\"];\n 23 -->|output1| 24;\n 25[\"Samtools calmd\"];\n 24 -->|output_bam| 25;\n 26[\"Samtools view\"];\n 25 -->|calmd_output| 26;\n 27[\"Samtools view\"];\n 25 -->|calmd_output| 27;\n 28[\"Select\"];\n 26 -->|outputsam| 28;\n 29[\"Replace Text\"];\n 28 -->|out_file1| 29;\n 30[\"Samtools view\"];\n 27 -->|outputsam| 30;\n 29 -->|outfile| 30;\n 31[\"Extract Tumor read\"];\n 30 -->|outputsam| 31;\n 32[\"Extract normal read\"];\n 30 -->|outputsam| 32;\n 33[\"Control-FREEC\"];\n 5 -->|output| 33;\n 32 -->|output| 33;\n 31 -->|output| 33;\n 2f4f45dd-d145-4078-aed9-5d832c51923b[\"Output\\nout_sample_info\"];\n 33 --> 2f4f45dd-d145-4078-aed9-5d832c51923b;\n style 2f4f45dd-d145-4078-aed9-5d832c51923b stroke:#2c3143,stroke-width:4px;\n 13edcdd6-d7f6-4e0f-976e-1032084accf1[\"Output\\nout_sample_coord\"];\n 33 --> 13edcdd6-d7f6-4e0f-976e-1032084accf1;\n style 13edcdd6-d7f6-4e0f-976e-1032084accf1 stroke:#2c3143,stroke-width:4px;\n ac78da9a-8aa8-45ce-a2d1-3c366783fa60[\"Output\\nout_control_raw\"];\n 33 --> ac78da9a-8aa8-45ce-a2d1-3c366783fa60;\n style ac78da9a-8aa8-45ce-a2d1-3c366783fa60 stroke:#2c3143,stroke-width:4px;\n 213ea0be-1ec6-469b-9556-69682bba69fe[\"Output\\nout_sample_raw\"];\n 33 --> 213ea0be-1ec6-469b-9556-69682bba69fe;\n style 213ea0be-1ec6-469b-9556-69682bba69fe stroke:#2c3143,stroke-width:4px;\n 59a99e4f-01ef-4118-8777-63707e8b1696[\"Output\\nout_ratio_log2_circos\"];\n 33 --> 59a99e4f-01ef-4118-8777-63707e8b1696;\n style 59a99e4f-01ef-4118-8777-63707e8b1696 stroke:#2c3143,stroke-width:4px;\n 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5[\"Output\\nout_chr_sorted_circos\"];\n 33 --> 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5;\n style 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5 stroke:#2c3143,stroke-width:4px;\n 662d214b-3d22-4f67-a4ef-a77b106d1535[\"Output\\nout_gc_profile\"];\n 33 --> 662d214b-3d22-4f67-a4ef-a77b106d1535;\n style 662d214b-3d22-4f67-a4ef-a77b106d1535 stroke:#2c3143,stroke-width:4px;\n 02c14e20-cccd-4804-bbb6-13323afeda2e[\"Output\\nout_mg_log2_png\"];\n 33 --> 02c14e20-cccd-4804-bbb6-13323afeda2e;\n style 02c14e20-cccd-4804-bbb6-13323afeda2e stroke:#2c3143,stroke-width:4px;\n 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7[\"Output\\nout_mg_png\"];\n 33 --> 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7;\n style 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7 stroke:#2c3143,stroke-width:4px;\n 14aba5a4-1ade-477e-b937-7714038f3fd3[\"Output\\nout_sample_subclones\"];\n 33 --> 14aba5a4-1ade-477e-b937-7714038f3fd3;\n style 14aba5a4-1ade-477e-b937-7714038f3fd3 stroke:#2c3143,stroke-width:4px;\n 61323e5f-7846-47e9-a0b3-d79f64ca2bd8[\"Output\\nout_sample_ratio\"];\n 33 --> 61323e5f-7846-47e9-a0b3-d79f64ca2bd8;\n style 61323e5f-7846-47e9-a0b3-d79f64ca2bd8 stroke:#2c3143,stroke-width:4px;\n 34[\"Circos\"];\n 33 -->|out_chr_sorted_circos| 34;\n 33 -->|out_ratio_log2_circos| 34;\n 23ea7d87-b936-4879-bfaa-beb1e141834e[\"Output\\noutput_png\"];\n 34 --> 23ea7d87-b936-4879-bfaa-beb1e141834e;\n style 23ea7d87-b936-4879-bfaa-beb1e141834e stroke:#2c3143,stroke-width:4px;",
- "modified": "2024-12-09 08:53:37 +0000",
+ "modified": "2024-12-13 13:26:19 +0000",
"name": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC",
"outputs": [
{
@@ -896362,26 +834503,6 @@
},
"admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n owner: iuc\n revisions: 836d1aa3e89a\n tool_panel_section_label: Graph/Display Data\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n owner: iuc\n revisions: c9a8ef2aa380\n tool_panel_section_label: Variant Calling\n tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
"api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
- "contributions": {
- "authorship": [
- "annasyme",
- "slugger70",
- "tseemann"
- ],
- "reviewing": [
- "jennaj",
- "hexylena",
- "bgruening",
- "shiltemann",
- "bebatut",
- "abretaud",
- "nsoranzo",
- "slugger70",
- "pvanheus",
- "njall",
- "mblue9"
- ]
- },
"contributors": [
{
"id": "annasyme",
@@ -896412,223 +834533,6 @@
"name": "Torsten Seemann",
"page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
"url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
- },
- {
- "contact_for_training": true,
- "email": "jen@galaxyproject.org",
- "id": "jennaj",
- "joined": "2018-06",
- "linkedin": "jennifer.hillman.jackson",
- "location": {
- "country": "US",
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- "lon": -122.0226576
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- "in_memoriam": "Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022\n\nHe was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.