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Merge list of tools to keep and to exclude in 1 file and add deprecation status #102

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Jun 3, 2024
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Merge branch 'main' of github.com:galaxyproject/galaxy_tool_metadata_…
…extractor into merge_keep_exclude_list
bebatut committed Jun 3, 2024
commit 3c6371d1f3c408e6d06aceeb2d39c56bfd5f6db3
4 changes: 2 additions & 2 deletions bin/extract_galaxy_tools.py
Original file line number Diff line number Diff line change
@@ -649,13 +649,13 @@ def filter_tools(
help="Filepath to TSV with all extracted tools, generated by extractools command",
)
filtertools.add_argument(
"--ts_filtered_tools",
"--ts-filtered-tools",
"-t",
required=True,
help="Filepath to TSV with tools filtered based on ToolShed category",
)
filtertools.add_argument(
"--filtered_tools",
"--filtered-tools",
"-f",
required=True,
help="Filepath to TSV with tools filtered based on ToolShed category and manual curation",
4 changes: 2 additions & 2 deletions bin/get_community_tools.sh
Original file line number Diff line number Diff line change
@@ -12,8 +12,8 @@ for com_data_fp in data/communities/* ; do
python bin/extract_galaxy_tools.py \
filtertools \
--tools "results/all_tools.tsv" \
--ts_filtered_tools "results/$community/tools_filtered_by_ts_categories.tsv" \
--filtered_tools "results/$community/tools.tsv" \
--ts-filtered-tools "results/$community/tools_filtered_by_ts_categories.tsv" \
--filtered-tools "results/$community/tools.tsv" \
--categories "data/communities/$community/categories" \
--status "data/communities/$community/tool_status.tsv"

18 changes: 9 additions & 9 deletions results/all_tools.tsv

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12 changes: 6 additions & 6 deletions results/microgalaxy/index.html
Original file line number Diff line number Diff line change
@@ -5240,7 +5240,7 @@
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree</td>
<td>2.3.3</td>
<td>2.3.4</td>
<td>iqtree</td>
<td>2.3.4</td>
<td>(1/1)</td>
@@ -6489,7 +6489,7 @@
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
<td>1.11</td>
<td>multiqc</td>
<td>1.22.1</td>
<td>1.22.2</td>
<td>(1/1)</td>
<td>(1/1)</td>
<td>(1/1)</td>
@@ -7734,7 +7734,7 @@
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit</td>
<td>2.8.1</td>
<td>2.8.2</td>
<td>seqkit</td>
<td>2.8.2</td>
<td>(0/5)</td>
@@ -8011,7 +8011,7 @@
<td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
<td>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.</td>
<td>spades</td>
<td>biosyntheticspades, coronaspades, plasmidspades, rnaspades, rnaviralspades, metaspades, metaplasmidspades, spades, metaviralspades</td>
<td>rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades</td>
<td></td>
<td>SPAdes</td>
<td>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.</td>
@@ -8568,14 +8568,14 @@
<td></td>
<td></td>
<td></td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/jonas-fuchs/virHEAT</td>
<td>Visualization, Variant Analysis</td>
<td>virheat</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat</td>
<td>0.6</td>
<td>0.7</td>
<td>virheat</td>
<td>0.7</td>
<td>(0/1)</td>
24 changes: 24 additions & 0 deletions results/microgalaxy/tools.tsv

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14 changes: 7 additions & 7 deletions results/repositories03.list_tools.tsv

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4 changes: 2 additions & 2 deletions results/repositories04.list_tools.tsv
Original file line number Diff line number Diff line change
@@ -220,12 +220,12 @@ sceasy sceasy_convert Convert scRNA data object between popular formats
scmap scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0. To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scmap 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/scmap 1.6.4 scmap-cli 0.1.0 (0/7) (0/7) (7/7) (0/7)
scpred scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0 To update Transcriptomics, RNA, Statistics, Sequence Analysis suite_scpred 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/scpred 1.0.2 scpred-cli 0.1.0 (0/4) (0/4) (4/4) (0/4)
seurat 1543.0 66.0 seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1 Up-to-date https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ Transcriptomics, RNA, Statistics, Sequence Analysis suite_seurat ebi-gxa https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat 4.0.0 seurat-scripts 4.0.0 (0/19) (0/19) (14/19) (11/19)
ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 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 1.0.0+galaxy1 ucsc-cell-browser 1.2.5 (0/1) (0/1) (1/1) (0/1)
ucsc-cell-browser ucsc_cell_browser Python pipeline and Javascript scatter plot library for single-cell datasets To update https://cells.ucsc.edu/ Transcriptomics ucsc_cell_browser 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 1.0.0+galaxy1 ucsc-cell-browser 1.2.6 (0/1) (0/1) (1/1) (0/1)
biotransformer biotransformer BioTransformer is a tool for prediction of small molecule metabolism in mammals. biotransformer biotransformer BioTransformer BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. Metabolic pathway prediction, PTM site prediction, Natural product identification Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR Up-to-date https://bitbucket.org/djoumbou/biotransformerjar/src/master/ Metabolomics biotransformer recetox https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer 3.0.20230403 biotransformer 3.0.20230403 (0/1) (1/1) (1/1) (1/1)
filter_compounds filter_orgmet_anorg Tool for filtering organometallics/anorganic compounds from a list of compounds. To update https://github.com/RECETOX/galaxytools/ Metabolomics filter_compounds recetox https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds 3.1.1 openbabel 2.3.90dev7d621d9 (0/1) (0/1) (0/1) (0/1)
gc_derivatization gc_derivatization In silico derivatization for GC. Up-to-date https://github.com/RECETOX/gc-meox-tms Metabolomics gc_derivatization recetox https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization 1.0.1 gc-meox-tms 1.0.1 (0/1) (0/1) (0/1) (0/1)
isolib isolib Create an isotopic pattern library for given compounds and adducts. To update https://github.com/RECETOX/galaxytools/ Metabolomics isolib recetox https://github.com/RECETOX/galaxytools/tree/master/tools/isolib https://github.com/RECETOX/galaxytools/tree/master/tools/isolib 1.0.1+galaxy0 bioconductor-metabocoreutils 1.10.0 (0/1) (0/1) (0/1) (0/1)
matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics To update https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.24.0 matchms 0.25.0 (2/13) (9/13) (13/13) (11/13)
matchms matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting Searching, filtering and converting mass spectral libraries. matchms matchms Matchms Tool to import, process, clean, and compare mass spectrometry data. Spectral library search, Format validation, Filtering Metabolomics Up-to-date https://github.com/matchms/matchms Metabolomics matchms recetox https://github.com/RECETOX/galaxytools/tree/master/tools/matchms https://github.com/RECETOX/galaxytools/tree/master/tools/matchms 0.25.0 matchms 0.25.0 (2/14) (9/14) (13/14) (11/14)
misc use_theoretical_mz_annotations To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/misc https://github.com/RECETOX/galaxytools/tree/master/tools/misc 1.0.0 (0/1) (0/1) (1/1) (0/1)
msmetaenhancer 103.0 1.0 msmetaenhancer msmetaenhancer msmetaenhancer MSMetaEnhancer Tool for mass spectra metadata annotation. Annotation, Standardisation and normalisation Metabolomics, Compound libraries and screening, Data submission, annotation and curation Up-to-date https://github.com/RECETOX/MSMetaEnhancer Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer 0.4.0 msmetaenhancer 0.4.0 (0/1) (1/1) (1/1) (1/1)
msp_merge msp_merge To update https://github.com/RECETOX/galaxytools Metabolomics recetox https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge 0.1.0 matchms 0.25.0 (0/1) (0/1) (0/1) (0/1)
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