diff --git a/asaim.yaml b/asaim.yaml index 086902f6..5073ad7c 100644 --- a/asaim.yaml +++ b/asaim.yaml @@ -118,7 +118,7 @@ tools: - name: 'interproscan5' owner: 'bgruening' - tool_panel_section_label: 'Metagenomic Analysis' + tool_panel_section_label: 'Annotation' # combination_taxo_func - name: 'combine_metaphlan2_humann2' @@ -133,10 +133,10 @@ tools: - name: 'taxonomy_krona_chart' owner: 'crs4' - tool_panel_section_label: 'Graph/Display Data' + tool_panel_section_label: 'Metagenomic Analysis' # AMR - name: 'kleborate' + - name: 'kleborate' owner: 'iuc' tool_panel_section_label: 'Metagenomic Analysis' diff --git a/asaim.yaml.lock b/asaim.yaml.lock index 7e9c0ecd..5fbf5e29 100644 --- a/asaim.yaml.lock +++ b/asaim.yaml.lock @@ -215,7 +215,7 @@ tools: owner: bgruening revisions: - 82547f0d3a29 - tool_panel_section_label: Metagenomic Analysis + tool_panel_section_label: Annotation - name: combine_metaphlan2_humann2 owner: bebatut revisions: diff --git a/bgruening.yaml b/bgruening.yaml index 94cfbb61..ad179bf7 100644 --- a/bgruening.yaml +++ b/bgruening.yaml @@ -273,7 +273,7 @@ tools: - name: format_cd_hit_output owner: bebatut - tool_panel_section_label: Metagenomic Analysis + tool_panel_section_label: Multiple Alignments - name: format_metaphlan2_output owner: bebatut diff --git a/bgruening.yaml.lock b/bgruening.yaml.lock index fd51c8b5..03537831 100644 --- a/bgruening.yaml.lock +++ b/bgruening.yaml.lock @@ -909,7 +909,7 @@ tools: owner: bebatut revisions: - 64da677bcee2 - tool_panel_section_label: Metagenomic Analysis + tool_panel_section_label: Multiple Alignments - name: format_metaphlan2_output owner: bebatut revisions: diff --git a/cheminformatics.yaml b/cheminformatics.yaml index bc45279b..91d53b6a 100644 --- a/cheminformatics.yaml +++ b/cheminformatics.yaml @@ -31,19 +31,19 @@ tools: - name: ctb_im_cluster_butina owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: ctb_im_standardize owner: bgruening - tool_panel_section_label: ChemicalToolBox + tool_panel_section_label: ChemicalToolBox - name: ctb_im_o3dalign owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: ctb_im_cluster_butina_matrix owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: traj_selections_and_merge owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -51,18 +51,18 @@ tools: - name: ctb_im_constrained_conf_gen owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: ctb_im_conformers owner: bgruening - tool_panel_section_label: ChemicalToolBox + tool_panel_section_label: ChemicalToolBox - name: ctb_im_rxn_smarts_filter owner: bgruening - tool_panel_section_label: ChemicalToolBox + tool_panel_section_label: ChemicalToolBox - name: ctb_im_pbf_ev owner: bgruening - tool_panel_section_label: ChemicalToolBox + tool_panel_section_label: ChemicalToolBox - name: openduck_run_smd owner: bgruening @@ -139,7 +139,7 @@ tools: - name: padel owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: md_converter owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -158,7 +158,7 @@ tools: - name: gmx_md owner: chemteam - tool_panel_section_label: ChemicalToolBox + tool_panel_section_label: ChemicalToolBox - name: gmx_merge_topology_files owner: chemteam @@ -168,11 +168,11 @@ tools: owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: gmx_fep + - name: gmx_fep owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: gmx_trj + - name: gmx_trj owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -184,22 +184,22 @@ tools: owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: gmx_makendx + - name: gmx_makendx owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: gmx_editconf + - name: gmx_editconf owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: gmx_check + - name: gmx_check owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: alchemical_analysis + - name: alchemical_analysis owner: chemteam tool_panel_section_label: ChemicalToolBox - + - name: ctb_rdkit_descriptors owner: bgruening tool_panel_section_label: ChemicalToolBox @@ -211,7 +211,7 @@ tools: - name: mdanalysis_angle owner: chemteam tool_panel_section_label: ChemicalToolBox - + - name: mdanalysis_rdf owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -244,7 +244,7 @@ tools: owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: acpype_amber2gromacs + - name: acpype_amber2gromacs owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -263,12 +263,12 @@ tools: - name: bio3d_rmsd owner: chemteam tool_panel_section_label: ChemicalToolBox - + - name: bio3d_pca owner: chemteam tool_panel_section_label: ChemicalToolBox - - name: bio3d_pca_visualize + - name: bio3d_pca_visualize owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -299,11 +299,11 @@ tools: - name: openbabel_remsmall owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_obgrep owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_change_title owner: bgruening tool_panel_section_label: ChemicalToolBox @@ -311,31 +311,31 @@ tools: - name: openbabel_genprop owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_remions owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_multi_obgrep owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_svg_depiction owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_spectrophore_search owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_remove_protonation_state owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_compound_convert owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_subsearch owner: bgruening tool_panel_section_label: ChemicalToolBox @@ -343,11 +343,11 @@ tools: - name: openbabel_filter owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_addh owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: openbabel_remduplicates owner: bgruening tool_panel_section_label: ChemicalToolBox @@ -391,15 +391,15 @@ tools: - name: ambertools_parmchk2 owner: chemteam tool_panel_section_label: ChemicalToolBox - + - name: chembl owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: chembl_structure_pipeline owner: bgruening tool_panel_section_label: ChemicalToolBox - + - name: fpocket owner: bgruening tool_panel_section_label: ChemicalToolBox @@ -427,11 +427,11 @@ tools: - name: smina owner: earlhaminst tool_panel_section_label: ChemicalToolBox - + - name: gmx_rg owner: chemteam tool_panel_section_label: ChemicalToolBox - + - name: acpype_amber2gromacs owner: chemteam tool_panel_section_label: ChemicalToolBox @@ -454,4 +454,4 @@ tools: - name: gmx_rmsf owner: chemteam - tool_panel_section_label: ChemicalToolBox \ No newline at end of file + tool_panel_section_label: ChemicalToolBox diff --git a/climate.yaml b/climate.yaml index ba8d47cd..57ef4b23 100644 --- a/climate.yaml +++ b/climate.yaml @@ -79,11 +79,9 @@ tools: - name: gdal_gdaladdo owner: ecology tool_panel_section_label: 'GIS Data Handling' - - name: gdal_gdalbuildvrt owner: ecology tool_panel_section_label: 'GIS Data Handling' - - name: gdal_gdalinfo owner: ecology tool_panel_section_label: 'GIS Data Handling' @@ -99,27 +97,23 @@ tools: - name: gdal_gdalwarp owner: ecology tool_panel_section_label: 'GIS Data Handling' - - name: gdal_ogr2ogr owner: ecology tool_panel_section_label: 'GIS Data Handling' - name: gdal_ogrinfo owner: ecology - tool_panel_section_label: 'GIS Data Handling' + tool_panel_section_label: 'GIS Data Handling' - name: spocc_occ owner: ecology tool_panel_section_label: 'Get Data' - - name: datamash_ops owner: iuc tool_panel_section_label: 'Join, Subtract and Group' - - name: datamash_reverse owner: iuc tool_panel_section_label: 'Join, Subtract and Group' - - name: datamash_transpose owner: iuc tool_panel_section_label: 'Join, Subtract and Group' diff --git a/cpt.yaml b/cpt.yaml index e8d3179f..b28e1d1a 100644 --- a/cpt.yaml +++ b/cpt.yaml @@ -7,43 +7,43 @@ tools: - name: cpt_fasta_remove_id owner: cpt tool_panel_section_label: FASTA/FASTQ - + - name: cpt_get_orfs owner: cpt tool_panel_section_label: Annotation - + - name: cpt_convert_mga owner: cpt tool_panel_section_label: Convert Formats - + - name: cpt_gff_add_parents owner: cpt tool_panel_section_label: Annotation - + - name: cpt_fix_aragorn owner: cpt tool_panel_section_label: Convert Formats - + - name: cpt_fix_sixpack owner: cpt tool_panel_section_label: Annotation - + - name: cpt_shinefind owner: cpt tool_panel_section_label: Annotation - + - name: cpt_type_filter owner: cpt tool_panel_section_label: Annotation - + - name: cpt_req_phage_start owner: cpt tool_panel_section_label: Annotation - + - name: cpt_remove_annotations owner: cpt tool_panel_section_label: Annotation - + - name: cpt_prep_for_apollo owner: cpt tool_panel_section_label: Annotation @@ -63,7 +63,7 @@ tools: - name: cpt_lipory owner: cpt tool_panel_section_label: Annotation - + - name: cpt_intersect_adjacent owner: cpt tool_panel_section_label: Annotation diff --git a/earlhaminst.yaml b/earlhaminst.yaml index 4e67cb4d..10df0bb9 100644 --- a/earlhaminst.yaml +++ b/earlhaminst.yaml @@ -22,7 +22,7 @@ tools: tool_panel_section_label: Phylogenetics - name: hcluster_sg_parser - owner: earlhaminst + owner: earlhaminst tool_panel_section_label: Phylogenetics - name: t_coffee @@ -36,11 +36,11 @@ tools: - name: gafa owner: earlhaminst tool_panel_section_label: Phylogenetics - + - name: gstf_preparation owner: earlhaminst tool_panel_section_label: Phylogenetics - + - name: ete owner: earlhaminst tool_panel_section_label: Phylogenetics @@ -52,7 +52,7 @@ tools: - name: ensembl_get_feature_info owner: earlhaminst tool_panel_section_label: Get Data - + - name: ensembl_get_genetree owner: earlhaminst tool_panel_section_label: Get Data diff --git a/ecology.yaml b/ecology.yaml index a82697b5..74cc254f 100644 --- a/ecology.yaml +++ b/ecology.yaml @@ -6,15 +6,15 @@ tools: - name: pampa_presabs owner: ecology tool_panel_section_label: 'Species abundance' - + - name: pampa_communitymetrics owner: ecology tool_panel_section_label: 'Species abundance' - + - name: pampa_glmsp owner: ecology tool_panel_section_label: 'Species abundance' - + - name: pampa_glmcomm owner: ecology tool_panel_section_label: 'Species abundance' @@ -22,27 +22,27 @@ tools: - name: pampa_plotglm owner: ecology tool_panel_section_label: 'Species abundance' - + - name: stoc_maketable owner: ecology tool_panel_section_label: 'Species abundance' - + - name: stoc_filteringsp owner: ecology tool_panel_section_label: 'Species abundance' - + - name: stoc_mainglm owner: ecology tool_panel_section_label: 'Species abundance' - + - name: stoc_mainglm_group owner: ecology tool_panel_section_label: 'Species abundance' - + - name: stoc_trend_indic owner: ecology tool_panel_section_label: 'Species abundance' - + - name: regionalgam_ab_index owner: ecology tool_panel_section_label: 'Species abundance' @@ -98,14 +98,14 @@ tools: - name: cb_div owner: ecology tool_panel_section_label: 'Biodiversity data exploration' - + - name: cb_dissim owner: ecology - tool_panel_section_label: 'Biodiversity data exploration' - + tool_panel_section_label: 'Compute indicators for turnover boulders fields' + - name: cb_ivr owner: ecology - tool_panel_section_label: 'Biodiversity data exploration' + tool_panel_section_label: 'Compute indicators for turnover boulders fields' - name: sample_seqs owner: peterjc @@ -145,7 +145,7 @@ tools: - name: prinseq owner: iuc - tool_panel_section_label: 'Text Manipulation' + tool_panel_section_label: 'FASTA/FASTQ' - name: split_file_on_column @@ -175,7 +175,7 @@ tools: - name: subtract owner: devteam - tool_panel_section_label: 'Text Manipulation' + tool_panel_section_label: 'Operate on Genomic Intervals' - name: subtract_query owner: devteam @@ -211,7 +211,7 @@ tools: - name: cluster owner: devteam - tool_panel_section_label: 'Text Manipulation' + tool_panel_section_label: 'Operate on Genomic Intervals' - name: get_flanks owner: devteam @@ -219,11 +219,11 @@ tools: - name: complement owner: devteam - tool_panel_section_label: 'Text Manipulation' + tool_panel_section_label: 'Operate on Genomic Intervals' - name: basecoverage owner: devteam - tool_panel_section_label: 'Text Manipulation' + tool_panel_section_label: 'Operate on Genomic Intervals' - name: dna_filtering owner: devteam @@ -642,7 +642,7 @@ tools: - name: xarray_metadata_info owner: ecology tool_panel_section_label: 'GIS Data Handling' - + - name: xarray_select owner: ecology tool_panel_section_label: 'GIS Data Handling' @@ -725,43 +725,43 @@ tools: - name: vigiechiro_idvalid owner: ecology tool_panel_section_label: 'Animal Detection on Acoustic Recordings' - + - name: cb_dissim owner: ecology tool_panel_section_label: 'Compute indicators for turnover boulders fields' - + - name: cb_ivr owner: ecology tool_panel_section_label: 'Compute indicators for turnover boulders fields' - + - name: champ_blocs owner: ecology tool_panel_section_label: 'Compute indicators for turnover boulders fields' - + - name: srs_preprocess_s2 owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_diversity_maps owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_global_indices owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_process_data owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_spectral_indices owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_pca owner: ecology tool_panel_section_label: 'Compute indicators for satellite remote sensing' - + - name: srs_metadata owner: ecology tool_panel_section_label: 'GIS Data Handling' @@ -769,11 +769,11 @@ tools: - name: obisindicators owner: ecology tool_panel_section_label: 'Biodiversity data exploration' - + - name: ab1_fastq_converter owner: ecology tool_panel_section_label: 'Convert Formats' - + - name: aligned_to_consensus owner: ecology tool_panel_section_label: 'Assembly' @@ -793,7 +793,7 @@ tools: - name: ecoregion_taxa_seeker owner: ecology tool_panel_section_label: 'Ecoregionalization' - + - name: ecoregion_eco_map owner: ecology tool_panel_section_label: 'Ecoregionalization' diff --git a/ecology.yaml.lock b/ecology.yaml.lock index a0ee7616..298fbd8c 100644 --- a/ecology.yaml.lock +++ b/ecology.yaml.lock @@ -147,14 +147,14 @@ tools: - 7e6cc3da1189 - 8dc082da41c1 - ffaa9a71b2d2 - tool_panel_section_label: Biodiversity data exploration + tool_panel_section_label: Compute indicators for turnover boulders fields - name: cb_ivr owner: ecology revisions: - 8c6142630659 - b67730406f1b - bcbad4f83dec - tool_panel_section_label: Biodiversity data exploration + tool_panel_section_label: Compute indicators for turnover boulders fields - name: sample_seqs owner: peterjc revisions: @@ -227,7 +227,7 @@ tools: - 02befcb391f5 - 1ee282794de3 - 654b3a274ed5 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: FASTA/FASTQ - name: split_file_on_column owner: bgruening revisions: @@ -271,7 +271,7 @@ tools: revisions: - 0145969324c4 - 0427ca314f3d - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract_query owner: devteam revisions: @@ -319,7 +319,7 @@ tools: revisions: - 05696474ee89 - a126ec6ea0e4 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: get_flanks owner: devteam revisions: @@ -330,13 +330,13 @@ tools: revisions: - 38c8bb402872 - 8b6c6ec55c6e - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: basecoverage owner: devteam revisions: - 2cedec3759e4 - 9c5ff4695c97 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: dna_filtering owner: devteam revisions: diff --git a/eirene.yaml b/eirene.yaml index e81d94bc..910bedd0 100644 --- a/eirene.yaml +++ b/eirene.yaml @@ -66,39 +66,39 @@ tools: - name: matchms_convert owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_filtering owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_fingerprint_similarity owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_formatter owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_metadata_export owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_metadata_match owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_networking owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_similarity owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_spectral_similarity owner: recetox tool_panel_section_label: Metabolomics - + - name: matchms_split owner: recetox tool_panel_section_label: Metabolomics diff --git a/europe-custom.yaml b/europe-custom.yaml index f97136b4..0f972a21 100644 --- a/europe-custom.yaml +++ b/europe-custom.yaml @@ -78,7 +78,7 @@ tools: - name: taxonomy_krona_chart owner: crs4 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: text_processing owner: bgruening @@ -110,7 +110,7 @@ tools: tool_panel_section_label: Get Data - name: prinseq owner: iuc - tool_panel_section_label: Text Manipulation + tool_panel_section_label: FASTA/FASTQ - name: add_value owner: devteam tool_panel_section_label: Text Manipulation @@ -149,19 +149,19 @@ tools: tool_panel_section_label: Text Manipulation - name: cluster owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: get_flanks owner: devteam tool_panel_section_label: Text Manipulation - name: complement owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: basecoverage owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract_query owner: devteam tool_panel_section_label: Text Manipulation @@ -190,16 +190,16 @@ tools: owner: iuc tool_panel_section_label: Join, Subtract and Group - # - install_repository_dependencies: true - # install_resolver_dependencies: true - # install_tool_dependencies: false - # name: datamash_wrapper - # owner: agordon - # tool_panel_section_label: Join, Subtract and Group + # - install_repository_dependencies: true + # install_resolver_dependencies: true + # install_tool_dependencies: false + # name: datamash_wrapper + # owner: agordon + # tool_panel_section_label: Join, Subtract and Group - name: subtract owner: devteam - tool_panel_section_label: Join, Subtract and Group + tool_panel_section_label: Operate on Genomic Intervals - name: bam_to_scidx owner: iuc @@ -323,7 +323,7 @@ tools: tool_panel_section_label: Regional Variation - name: draw_stacked_barplots owner: devteam - tool_panel_section_label: Regional Variation + tool_panel_section_label: Graph/Display Data - name: delete_overlapping_indels owner: devteam tool_panel_section_label: Regional Variation @@ -819,10 +819,10 @@ tools: tool_panel_section_label: Peak Calling - name: pileometh owner: bgruening - tool_panel_section_label: Epigenetics + tool_panel_section_label: Peak Calling - name: bwameth owner: iuc - tool_panel_section_label: Epigenetics + tool_panel_section_label: Mapping - name: metilene owner: rnateam tool_panel_section_label: Epigenetics @@ -876,7 +876,7 @@ tools: tool_panel_section_label: Annotation - name: hammock owner: hammock - tool_panel_section_label: Annotation + tool_panel_section_label: Multiple Alignments - name: segmentation_fold owner: yhoogstrate tool_panel_section_label: Annotation @@ -999,7 +999,7 @@ tools: tool_panel_section_label: ChemicalToolBox - name: hifive owner: sauria - tool_panel_section_label: Test Tools + tool_panel_section_label: Epigenetics - name: translate_bed_sequences owner: jjohnson tool_panel_section_label: Operate on Genomic Intervals @@ -1017,34 +1017,34 @@ tools: tool_panel_section_label: EMBOSS - name: kraken_taxonomy_report owner: iuc - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: ncbi_blast_plus owner: devteam tool_panel_section_label: NCBI Blast - name: kraken2tax owner: devteam - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken owner: devteam - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: blast_rbh owner: peterjc tool_panel_section_label: NCBI Blast - name: kraken_report owner: devteam - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: taxonomy_krona_chart owner: crs4 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken_filter owner: devteam - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken_translate owner: devteam - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: sample_seqs owner: peterjc - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Filter and Sort - name: diamond owner: bgruening tool_panel_section_label: NCBI Blast diff --git a/europe-custom.yaml.lock b/europe-custom.yaml.lock index 0ceb2aeb..1d637607 100644 --- a/europe-custom.yaml.lock +++ b/europe-custom.yaml.lock @@ -111,7 +111,7 @@ tools: owner: crs4 revisions: - 020b3087d0b7 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: text_processing owner: bgruening revisions: @@ -177,7 +177,7 @@ tools: - 1ee282794de3 - 654b3a274ed5 - 6b865dde1baa - tool_panel_section_label: Text Manipulation + tool_panel_section_label: FASTA/FASTQ - name: add_value owner: devteam revisions: @@ -242,7 +242,7 @@ tools: owner: devteam revisions: - 765ceb06c3e2 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: get_flanks owner: devteam revisions: @@ -252,17 +252,17 @@ tools: owner: devteam revisions: - e0a23ab32d7f - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract owner: devteam revisions: - 7a2a604ae9c8 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: basecoverage owner: devteam revisions: - 0a3e3133b09d - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract_query owner: devteam revisions: @@ -316,7 +316,7 @@ tools: owner: devteam revisions: - 7a2a604ae9c8 - tool_panel_section_label: Join, Subtract and Group + tool_panel_section_label: Operate on Genomic Intervals - name: bam_to_scidx owner: iuc revisions: @@ -554,7 +554,7 @@ tools: owner: devteam revisions: - e997b710e38a - tool_panel_section_label: Regional Variation + tool_panel_section_label: Graph/Display Data - name: delete_overlapping_indels owner: devteam revisions: @@ -1509,7 +1509,7 @@ tools: owner: bgruening revisions: - ccc755bdf11d - tool_panel_section_label: Epigenetics + tool_panel_section_label: Peak Calling - name: bwameth owner: iuc revisions: @@ -1521,7 +1521,7 @@ tools: - b4e6819b25ef - d82648ad25a3 - f7094efef903 - tool_panel_section_label: Epigenetics + tool_panel_section_label: Mapping - name: metilene owner: rnateam revisions: @@ -1624,7 +1624,7 @@ tools: owner: hammock revisions: - 4db310b7e37c - tool_panel_section_label: Annotation + tool_panel_section_label: Multiple Alignments - name: segmentation_fold owner: yhoogstrate revisions: @@ -1850,7 +1850,7 @@ tools: owner: sauria revisions: - 4a978cf8cf92 - tool_panel_section_label: Test Tools + tool_panel_section_label: Epigenetics - name: translate_bed_sequences owner: jjohnson revisions: @@ -1883,7 +1883,7 @@ tools: - 3f1a0d47ea8d - b11b3ac48bb9 - b97694b21bc3 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: ncbi_blast_plus owner: devteam revisions: @@ -1893,12 +1893,12 @@ tools: owner: devteam revisions: - f03c7ba8d8bc - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken owner: devteam revisions: - b2392a9dfb01 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: blast_rbh owner: peterjc revisions: @@ -1908,27 +1908,27 @@ tools: owner: devteam revisions: - 9ae975c30dde - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: taxonomy_krona_chart owner: crs4 revisions: - 020b3087d0b7 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken_filter owner: devteam revisions: - fe94f318048c - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: kraken_translate owner: devteam revisions: - b9971bca4b01 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Metagenomic Analysis - name: sample_seqs owner: peterjc revisions: - 02c13ef1a669 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: Filter and Sort - name: diamond owner: bgruening revisions: diff --git a/galaxy-australia.yaml b/galaxy-australia.yaml index 26bd29f0..d703d0e5 100644 --- a/galaxy-australia.yaml +++ b/galaxy-australia.yaml @@ -9,8 +9,8 @@ tools: - name: cactus_cactus owner: galaxy-australia - tool_panel_section_label: Assembly - + tool_panel_section_label: Assembly + - name: cactus_export owner: galaxy-australia tool_panel_section_label: Assembly diff --git a/goeckslab.yaml b/goeckslab.yaml index 8e53193f..529651e0 100644 --- a/goeckslab.yaml +++ b/goeckslab.yaml @@ -15,7 +15,7 @@ tools: - name: mesmer owner: goeckslab - tool_panel_section_label: Imaging + tool_panel_section_label: Spatial Omics - name: squidpy owner: goeckslab diff --git a/goeckslab.yaml.lock b/goeckslab.yaml.lock index 74cc932c..26e2cadb 100644 --- a/goeckslab.yaml.lock +++ b/goeckslab.yaml.lock @@ -18,7 +18,7 @@ tools: - 02abff468d60 - 187918c47051 - 53240d7c1fc5 - tool_panel_section_label: Imaging + tool_panel_section_label: Spatial Omics - name: squidpy owner: goeckslab revisions: diff --git a/imaging.yaml b/imaging.yaml index d455c8c3..00d56048 100644 --- a/imaging.yaml +++ b/imaging.yaml @@ -35,15 +35,15 @@ tools: - name: 2d_local_threshold owner: imgteam tool_panel_section_label: "Imaging" - + - name: segmetrics owner: imgteam tool_panel_section_label: "Imaging" - + - name: superdsm owner: imgteam tool_panel_section_label: "Imaging" - + - name: rfove owner: imgteam tool_panel_section_label: "Imaging" @@ -51,15 +51,15 @@ tools: - name: landmark_registration owner: imgteam tool_panel_section_label: "Imaging" - + - name: landmark_registration_ls owner: imgteam tool_panel_section_label: "Imaging" - + - name: image_registration_affine owner: imgteam tool_panel_section_label: "Imaging" - + - name: projective_transformation owner: imgteam tool_panel_section_label: "Imaging" @@ -67,19 +67,19 @@ tools: - name: projective_transformation_points owner: imgteam tool_panel_section_label: "Imaging" - + - name: spot_detection_2d owner: imgteam tool_panel_section_label: "Imaging" - + - name: points_association_nn owner: imgteam tool_panel_section_label: "Imaging" - + - name: curve_fitting owner: imgteam tool_panel_section_label: "Imaging" - + - name: imagecoordinates_flipaxis owner: imgteam tool_panel_section_label: "Imaging" @@ -87,7 +87,7 @@ tools: - name: 2d_split_binaryimage_by_watershed owner: imgteam tool_panel_section_label: "Imaging" - + - name: 2d_filter_segmentation_by_features owner: imgteam tool_panel_section_label: "Imaging" @@ -119,23 +119,23 @@ tools: - name: concat_channels owner: imgteam tool_panel_section_label: "Imaging" - + - name: points2binaryimage owner: imgteam tool_panel_section_label: "Imaging" - + - name: points2labelimage owner: imgteam tool_panel_section_label: "Imaging" - + - name: labelimage2points owner: imgteam tool_panel_section_label: "Imaging" - + - name: permutate_axis owner: imgteam tool_panel_section_label: "Imaging" - + - name: mahotas_features owner: imgteam tool_panel_section_label: "Imaging" @@ -143,11 +143,11 @@ tools: - name: 2d_feature_extraction owner: imgteam tool_panel_section_label: "Imaging" - + - name: count_objects owner: imgteam tool_panel_section_label: "Imaging" - + - name: coordinates_of_roi owner: imgteam tool_panel_section_label: "Imaging" @@ -175,7 +175,7 @@ tools: - name: visceral_evaluatesegmentation owner: imgteam tool_panel_section_label: "Imaging" - + - name: bfconvert owner: imgteam tool_panel_section_label: "Imaging" @@ -291,7 +291,7 @@ tools: - name: imagej2_bunwarpj_adapt_transform owner: imgteam tool_panel_section_label: "Imaging" - + - name: unzip owner: imgteam tool_panel_section_label: 'Collection Operations' @@ -303,91 +303,85 @@ tools: - name: cp_cellprofiler owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_common owner: bgruening - tool_panel_section_label: "Imaging" + tool_panel_section_label: "Imaging" - name: cp_color_to_gray owner: bgruening - tool_panel_section_label: "Imaging" + tool_panel_section_label: "Imaging" - name: cp_tile owner: bgruening - tool_panel_section_label: "Imaging" + tool_panel_section_label: "Imaging" - name: cp_track_objects owner: bgruening - tool_panel_section_label: "Imaging" + tool_panel_section_label: "Imaging" - name: cp_overlay_outlines owner: bgruening - tool_panel_section_label: "Imaging" + tool_panel_section_label: "Imaging" - name: cp_convert_objects_to_image owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_display_data_on_image owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_enhance_or_suppress_features owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_export_to_spreadsheet owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_gray_to_color owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_identify_primary_objects owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_mask_image owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_measure_granularity owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_measure_image_area_occupied owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_measure_image_intensity owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_measure_image_quality owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_measure_object_intensity owner: bgruening - tool_panel_section_label: "Imaging" - + tool_panel_section_label: "Imaging" - name: cp_measure_object_size_shape owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_measure_texture owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_relate_objects owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_save_images owner: bgruening tool_panel_section_label: "Imaging" - + - name: cp_image_math owner: bgruening tool_panel_section_label: "Imaging" diff --git a/metabolomics.yaml b/metabolomics.yaml index 70a006e2..eeafdd6b 100644 --- a/metabolomics.yaml +++ b/metabolomics.yaml @@ -52,7 +52,7 @@ tools: - name: camera_combinexsannos owner: mmonsoor tool_panel_section_label: Metabolomics - + - name: mspurity_flagremove owner: computational-metabolomics tool_panel_section_label: Metabolomics @@ -81,11 +81,11 @@ tools: - name: mspurity_createmsp owner: computational-metabolomics tool_panel_section_label: Metabolomics - + - name: mspurity_dimspredictpuritysingle owner: computational-metabolomics tool_panel_section_label: Metabolomics - + - name: mspurity_purityx owner: computational-metabolomics tool_panel_section_label: Metabolomics @@ -168,7 +168,7 @@ tools: - name: transformation owner: ethevenot - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: qualitymetrics owner: ethevenot @@ -183,15 +183,15 @@ tools: ## ALL - name: univariate owner: ethevenot - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: multivariate owner: ethevenot - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: anova owner: lecorguille - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: mixmodel4repeated_measures owner: jfrancoismartin @@ -203,7 +203,7 @@ tools: - name: biosigner owner: ethevenot - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: corr_table owner: melpetera @@ -211,7 +211,7 @@ tools: - name: heatmap owner: ethevenot - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics # annotation @@ -234,7 +234,7 @@ tools: - name: lcmsmatching owner: prog - tool_panel_section_label: Metabolomics + tool_panel_section_label: Annotation ## LCMS # - name: probmetab @@ -250,7 +250,7 @@ tools: - name: mspurity_spectralmatching owner: computational-metabolomics tool_panel_section_label: Metabolomics - + - name: metfrag owner: computational-metabolomics tool_panel_section_label: Metabolomics @@ -309,15 +309,15 @@ tools: - name: msconvert owner: galaxyp - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: thermo_raw_file_converter owner: galaxyp - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: msms_extractor owner: galaxyp - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: isoplot diff --git a/metabolomics.yaml.lock b/metabolomics.yaml.lock index 6b5f1468..1c4ce6f2 100644 --- a/metabolomics.yaml.lock +++ b/metabolomics.yaml.lock @@ -223,7 +223,7 @@ tools: owner: ethevenot revisions: - cc0e9eff0de2 - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: qualitymetrics owner: ethevenot revisions: @@ -240,18 +240,18 @@ tools: revisions: - 140290de7986 - 5687435b182c - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: multivariate owner: ethevenot revisions: - 5526f8258e8a - e91de3b04320 - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: anova owner: lecorguille revisions: - 102049093b7d - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: mixmodel4repeated_measures owner: jfrancoismartin revisions: @@ -267,7 +267,7 @@ tools: revisions: - b2414be87d4b - fa80bd02055f - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: corr_table owner: melpetera revisions: @@ -277,7 +277,7 @@ tools: owner: ethevenot revisions: - b1667c118127 - tool_panel_section_label: Metabolomics + tool_panel_section_label: Statistics - name: hmdb_ms_search owner: fgiacomoni revisions: @@ -304,7 +304,7 @@ tools: revisions: - f86fec07f392 - fb9c0409d85c - tool_panel_section_label: Metabolomics + tool_panel_section_label: Annotation - name: golm_ws_lib_search owner: fgiacomoni revisions: @@ -398,17 +398,17 @@ tools: revisions: - 6153e8ada1ee - 9ec469ff191a - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: thermo_raw_file_converter owner: galaxyp revisions: - 77a18a61aeed - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: msms_extractor owner: galaxyp revisions: - 4bef80b09854 - tool_panel_section_label: Metabolomics + tool_panel_section_label: Convert Formats - name: isoplot owner: workflow4metabolomics revisions: diff --git a/peterjc.yaml b/peterjc.yaml index ac46aaa5..67215e6f 100644 --- a/peterjc.yaml +++ b/peterjc.yaml @@ -11,7 +11,7 @@ tools: - name: sample_seqs owner: peterjc tool_panel_section_label: 'Filter and Sort' - + - name: seq_filter_by_id owner: peterjc tool_panel_section_label: 'Filter and Sort' diff --git a/rnateam.yaml b/rnateam.yaml index 6da48cad..cc50fdcf 100644 --- a/rnateam.yaml +++ b/rnateam.yaml @@ -38,48 +38,48 @@ tools: - name: cmv owner: rnateam - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: rnalien owner: rnateam - tool_panel_section_label: RNA Analysis + tool_panel_section_label: RNA Analysis - name: selectsequencesfrommsa owner: rnateam - tool_panel_section_label: RNA Analysis + tool_panel_section_label: RNA Analysis - name: locarna_multiple owner: rnateam - tool_panel_section_label: RNA Analysis + tool_panel_section_label: RNA Analysis - name: fuma owner: yhoogstrate - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: infernal owner: bgruening - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: aresite2 owner: rnateam - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: targetfinder owner: rnateam - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: flaimapper owner: yhoogstrate - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: nastiseq owner: rnateam - tool_panel_section_label: RNA Analysis - + tool_panel_section_label: RNA Analysis + - name: pipmir owner: rnateam tool_panel_section_label: RNA Analysis - + - name: ribotaper owner: rnateam tool_panel_section_label: RNA Analysis @@ -115,7 +115,7 @@ tools: - name: rnaz_randomize_aln owner: bgruening tool_panel_section_label: RNA Analysis - + - name: rnaz_annotate owner: bgruening tool_panel_section_label: RNA Analysis @@ -131,7 +131,7 @@ tools: - name: htseq_clip owner: rnateam tool_panel_section_label: Peak Calling - + - name: peakachu owner: rnateam tool_panel_section_label: Peak Calling diff --git a/single-cell-ebi-gxa.yaml b/single-cell-ebi-gxa.yaml index 255bea70..a14ce795 100644 --- a/single-cell-ebi-gxa.yaml +++ b/single-cell-ebi-gxa.yaml @@ -7,131 +7,131 @@ tools: - name: dropletutils_read_10x owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: dropletutils_empty_drops owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: gtf2gene_list owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: retrieve_scxa owner: ebi-gxa tool_panel_section_id: 'hca_sc_get-scrna' - + - name: hca_matrix_downloader owner: ebi-gxa tool_panel_section_id: 'hca_sc_get-scrna' - + - name: sc3_calc_biology owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: sc3_calc_consens owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: sc3_calc_dists owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: sc3_calc_transfs owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' -# + - name: sc3_estimate_k owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: sc3_kmeans owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: sc3_prepare owner: ebi-gxa tool_panel_section_id: 'hca_sc_sc3_tools' - + - name: anndata_ops owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_compute_graph owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_filter_cells owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_filter_genes owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_find_cluster owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_find_markers owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_find_variable_genes owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_normalise_data owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_parameter_iterator owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_plot_embed owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_plot_trajectory owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_read_10x owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_regress_variable owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_diffmap owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_dpt owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_fdg owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_paga owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_pca owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_tsne owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_run_umap owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_scale_data owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' @@ -139,15 +139,15 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_integrate_harmony owner: ebi-gxa - tool_panel_section_id: 'hca_sc_scanpy_tools' - + tool_panel_section_id: 'hca_sc_scanpy_tools' + - name: scanpy_integrate_mnn owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: scanpy_integrate_bbknn owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' @@ -163,119 +163,119 @@ tools: - name: scanpy_integrate_bbknn owner: ebi-gxa tool_panel_section_id: 'hca_sc_scanpy_tools' - + - name: seurat_create_seurat_object owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_dim_plot owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_export_cellbrowser owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_filter_cells owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_find_clusters owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_find_markers owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_find_variable_genes owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_normalise_data owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_read10x owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_run_pca owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_run_tsne owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_scale_data owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: seurat_find_neighbours owner: ebi-gxa tool_panel_section_id: 'hca_sc_seurat_tools' - + - name: monocle3_create owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_diffexp owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_learngraph owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_ordercells owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_partition owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_plotcells owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_preprocess owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_reducedim owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: monocle3_topmarkers owner: ebi-gxa tool_panel_section_id: 'hca_sc_monocle3_tools' - + - name: run_sccaf owner: ebi-gxa tool_panel_section_id: 'hca_sc_sccaf_tools' - + - name: sccaf_asses owner: ebi-gxa tool_panel_section_id: 'hca_sc_sccaf_tools' - + - name: sccaf_asses_merger owner: ebi-gxa tool_panel_section_id: 'hca_sc_sccaf_tools' - + - name: sccaf_regress_out owner: ebi-gxa tool_panel_section_id: 'hca_sc_sccaf_tools' - + - name: scmap_preprocess_sce owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' - + - name: scmap_index_cell owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' - + - name: scmap_index_cluster owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' @@ -287,39 +287,39 @@ tools: - name: scmap_scmap_cluster owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' - + - name: scmap_select_features owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' - + - name: scmap_get_std_output owner: ebi-gxa tool_panel_section_id: 'hca_sc_scmap_tools' - + - name: ucsc_cell_browser owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: sceasy_convert owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: text_processing owner: bgruening tool_panel_section_label: 'Text Manipulation' - + - name: umi_tools_count owner: iuc tool_panel_section_label: FASTA/FASTQ - + - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: droplet_barcode_plot owner: ebi-gxa tool_panel_section_id: 'hca_sc_utils_viz' - + - name: ct_build_cell_ontology_dict owner: ebi-gxa tool_panel_section_id: 'hca_sc_label_analysis_tools' @@ -391,7 +391,7 @@ tools: - name: scpred_preprocess_data owner: ebi-gxa tool_panel_section_id: 'hca_sc_scpred_tools' - + - name: scpred_predict_labels owner: ebi-gxa tool_panel_section_id: 'hca_sc_scpred_tools' @@ -403,23 +403,23 @@ tools: - name: scpred_traint_test_split owner: ebi-gxa tool_panel_section_id: 'hca_sc_scpred_tools' - + - name: scater_read_10x_results owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' - + - name: scater_normalize owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' - + - name: scater_is_outlier owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' - + - name: scater_filter owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' - + - name: scater_calculate_qc_metrics owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' @@ -427,4 +427,3 @@ tools: - name: scater_calculate_cpm owner: ebi-gxa tool_panel_section_id: 'hca_sc_scater_tools' - diff --git a/tools_galaxyp.yaml b/tools_galaxyp.yaml index 6061cda6..e38b2dfb 100644 --- a/tools_galaxyp.yaml +++ b/tools_galaxyp.yaml @@ -51,31 +51,31 @@ tools: - name: pyprophet_export owner: galaxyp tool_panel_section_label: Proteomics - + - name: pyprophet_subsample owner: galaxyp tool_panel_section_label: Proteomics - + - name: pyprophet_score owner: galaxyp tool_panel_section_label: Proteomics - + - name: pyprophet_protein owner: galaxyp tool_panel_section_label: Proteomics - + - name: pyprophet_peptide owner: galaxyp tool_panel_section_label: Proteomics - + - name: pyprophet_merge owner: galaxyp tool_panel_section_label: Proteomics - - - name: msstatstmt + + - name: msstatstmt owner: galaxyp tool_panel_section_label: Proteomics - + - name: diffacto owner: galaxyp tool_panel_section_label: Proteomics @@ -83,7 +83,7 @@ tools: - name: msstats owner: galaxyp tool_panel_section_label: Proteomics - + - name: uniprotxml_downloader owner: galaxyp tool_panel_section_label: Get Data @@ -219,7 +219,7 @@ tools: - name: cardinal_combine owner: galaxyp tool_panel_section_label: Proteomics - + - name: qupath_roi_splitter owner: galaxyp tool_panel_section_label: Proteomics @@ -235,7 +235,7 @@ tools: - name: eggnog_mapper owner: galaxyp tool_panel_section_label: Proteomics - + - name: protein_properties owner: bgruening tool_panel_section_label: Proteomics @@ -254,7 +254,7 @@ tools: - name: idpquery owner: galaxyp - tool_panel_section_label: Proteomics + tool_panel_section_label: Convert Formats - name: proteomics_moff owner: galaxyp @@ -282,32 +282,32 @@ tools: - name: pep_pointer owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_db owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_expand owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_filter owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_sample owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_stat owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: metaquantome_viz owner: galaxyp - tool_panel_section_label: Proteomics - + tool_panel_section_label: Proteomics + - name: maxbin2 owner: mbernt tool_panel_section_label: Metagenomic Analysis @@ -315,31 +315,31 @@ tools: - name: msms_extractor owner: galaxyp tool_panel_section_label: Convert Formats - + - name: peptide_genomic_coordinate owner: galaxyp tool_panel_section_label: Proteomics - + - name: quantwiz_iq owner: galaxyp tool_panel_section_label: Proteomics - + - name: sixgill owner: galaxyp tool_panel_section_label: Metagenomic Analysis - + - name: metagene_annotator owner: galaxyp tool_panel_section_label: Metagenomic Analysis - + - name: pepquery owner: galaxyp tool_panel_section_label: Proteomics - + - name: mt2mq owner: galaxyp tool_panel_section_label: Proteomics - + - name: openms_rnadigestor owner: galaxyp tool_panel_section_label: Proteomics @@ -983,16 +983,16 @@ tools: - name: openms_databasefilter owner: galaxyp tool_panel_section_label: Proteomics - - + + - name: psm_validation owner: galaxyp tool_panel_section_label: Proteomics - + - name: meta_proteome_analyzer owner: galaxyp tool_panel_section_label: Proteomics - + - name: fastg2protlib owner: galaxyp tool_panel_section_label: Proteomics diff --git a/tools_galaxyp.yaml.lock b/tools_galaxyp.yaml.lock index aba2ad8c..ac537b91 100644 --- a/tools_galaxyp.yaml.lock +++ b/tools_galaxyp.yaml.lock @@ -602,7 +602,7 @@ tools: - 51d54a9c9283 - 66c38e74d1ae - 6da05a8b5d8b - tool_panel_section_label: Proteomics + tool_panel_section_label: Convert Formats - name: proteomics_moff owner: galaxyp revisions: diff --git a/tools_iuc.yaml b/tools_iuc.yaml index 6e5dcb4c..5816fbf4 100644 --- a/tools_iuc.yaml +++ b/tools_iuc.yaml @@ -186,7 +186,7 @@ tools: - name: homer_annotatepeaks owner: iuc tool_panel_section_label: Annotation - + - name: homer_findmotifs owner: iuc tool_panel_section_label: Annotation @@ -657,7 +657,7 @@ tools: - name: bwameth owner: iuc - tool_panel_section_label: Epigenetics + tool_panel_section_label: Mapping - name: moabs owner: iuc @@ -758,7 +758,7 @@ tools: - name: bbtools_bbduk owner: iuc tool_panel_section_label: FASTA/FASTQ - + - name: bbtools_bbmerge owner: iuc tool_panel_section_label: FASTA/FASTQ @@ -993,23 +993,23 @@ tools: - name: umi_tools_dedup owner: iuc - tool_panel_section_label: FASTA/FASTQ + tool_panel_section_label: FASTA/FASTQ - name: umi_tools_extract owner: iuc - tool_panel_section_label: FASTA/FASTQ + tool_panel_section_label: FASTA/FASTQ - name: umi_tools_group owner: iuc - tool_panel_section_label: FASTA/FASTQ + tool_panel_section_label: FASTA/FASTQ - name: umi_tools_whitelist owner: iuc - tool_panel_section_label: FASTA/FASTQ + tool_panel_section_label: FASTA/FASTQ - name: fasta_regex_finder owner: mbernt - tool_panel_section_label: FASTA/FASTQ + tool_panel_section_label: FASTA/FASTQ # FILTER AND SORT @@ -1516,7 +1516,7 @@ tools: - name: subtract owner: devteam - tool_panel_section_label: Join, Subtract and Group + tool_panel_section_label: Operate on Genomic Intervals # MACHINE LEARNING @@ -1878,10 +1878,10 @@ tools: - name: data_manager_build_bracken_database owner: iuc - - name: amrfinderplus_data_manager_build + - name: amrfinderplus_data_manager_build owner: iuc - - name: data_manager_bakta + - name: data_manager_bakta owner: iuc - name: drep_compare @@ -2894,7 +2894,7 @@ tools: - name: bbtools_bbduk owner: iuc - tool_panel_section_label: NCBI Blast + tool_panel_section_label: FASTA/FASTQ - name: diamond owner: bgruening @@ -3465,7 +3465,7 @@ tools: - name: migmap owner: iuc tool_panel_section_label: RNA Analysis - + - name: mirnature owner: iuc tool_panel_section_label: RNA Analysis @@ -3488,7 +3488,7 @@ tools: - name: rnaquast owner: iuc - tool_panel_section_label: RNA Analysis + tool_panel_section_label: Assembly - name: rseqc owner: nilesh @@ -3611,7 +3611,7 @@ tools: - name: draw_stacked_barplots owner: devteam - tool_panel_section_label: Regional Variation + tool_panel_section_label: Graph/Display Data - name: featurecounter owner: devteam @@ -3986,7 +3986,7 @@ tools: owner: iuc tool_panel_section_label: Statistics - ## IWtomic - Interval-Wise Testing for Omics Data + ## IWtomic - Interval-Wise Testing for Omics Data - name: iwtomics_loadandplot owner: iuc @@ -4041,11 +4041,11 @@ tools: - name: basecoverage owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: cluster owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: column_maker owner: devteam @@ -4109,7 +4109,7 @@ tools: - name: prinseq owner: iuc - tool_panel_section_label: Text Manipulation + tool_panel_section_label: FASTA/FASTQ - name: query_tabular owner: iuc @@ -4125,7 +4125,7 @@ tools: - name: subtract owner: devteam - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract_query owner: devteam @@ -4788,7 +4788,7 @@ tools: - name: data_manager_semibin owner: iuc - - name: data_manager_vep_cache_downloader + - name: data_manager_vep_cache_downloader owner: iuc - name: data_manager_pharokka diff --git a/tools_iuc.yaml.lock b/tools_iuc.yaml.lock index 4f485cf6..163a0d0e 100644 --- a/tools_iuc.yaml.lock +++ b/tools_iuc.yaml.lock @@ -1344,7 +1344,7 @@ tools: - b4e6819b25ef - d82648ad25a3 - f7094efef903 - tool_panel_section_label: Epigenetics + tool_panel_section_label: Mapping - name: moabs owner: iuc revisions: @@ -3261,7 +3261,7 @@ tools: - 0427ca314f3d - 5bc2dacbe729 - 7a2a604ae9c8 - tool_panel_section_label: Join, Subtract and Group + tool_panel_section_label: Operate on Genomic Intervals - name: deepmicro owner: iuc revisions: @@ -6293,7 +6293,7 @@ tools: - 204a131e47db - 425dab0e057b - a9c9d768b751 - tool_panel_section_label: NCBI Blast + tool_panel_section_label: FASTA/FASTQ - name: diamond owner: bgruening revisions: @@ -6933,7 +6933,7 @@ tools: owner: iuc revisions: - 02f0dfb10421 - - 0407236012e5 + - 4072360120e4 - 1d9d3c6bc246 - 6d29207a32c5 - 6fede7bd6c8f @@ -7890,7 +7890,7 @@ tools: - 96f74538896e - e989670c7fc7 - f89e3c318453 - tool_panel_section_label: RNA Analysis + tool_panel_section_label: Assembly - name: rseqc owner: nilesh revisions: @@ -8201,7 +8201,7 @@ tools: owner: devteam revisions: - e997b710e38a - tool_panel_section_label: Regional Variation + tool_panel_section_label: Graph/Display Data - name: featurecounter owner: devteam revisions: @@ -9069,7 +9069,7 @@ tools: - 1e6a9e97fa41 - 2cedec3759e4 - 9c5ff4695c97 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: cluster owner: devteam revisions: @@ -9077,7 +9077,7 @@ tools: - 765ceb06c3e2 - a126ec6ea0e4 - d5677eecbad4 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: column_maker owner: devteam revisions: @@ -9190,7 +9190,7 @@ tools: - 1ee282794de3 - 654b3a274ed5 - 6b865dde1baa - tool_panel_section_label: Text Manipulation + tool_panel_section_label: FASTA/FASTQ - name: query_tabular owner: iuc revisions: @@ -9214,7 +9214,7 @@ tools: - 0427ca314f3d - 5bc2dacbe729 - 7a2a604ae9c8 - tool_panel_section_label: Text Manipulation + tool_panel_section_label: Operate on Genomic Intervals - name: subtract_query owner: devteam revisions: