From e308edef0ee6d173c37af36a155318a6788bbdfb Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 5 Dec 2025 14:53:13 +0100 Subject: [PATCH] manually curate some sections and tools --- usegalaxy.cz/annotation.yml | 16 ++++++ usegalaxy.cz/annotation.yml.lock | 50 +++++++++++++++++ usegalaxy.cz/assembly.yml | 12 ++++ usegalaxy.cz/assembly.yml.lock | 41 ++++++++++++++ usegalaxy.cz/bed.yml.lock | 1 + usegalaxy.cz/chemicaltoolbox.yml | 6 ++ usegalaxy.cz/chemicaltoolbox.yml.lock | 24 ++++++++ usegalaxy.cz/collection_operations.yml.lock | 2 + usegalaxy.cz/convert_formats.yml | 4 ++ usegalaxy.cz/convert_formats.yml.lock | 14 +++++ usegalaxy.cz/epigenetics.yml.lock | 4 ++ usegalaxy.cz/fasta_fastq.yml | 8 +++ usegalaxy.cz/fasta_fastq.yml.lock | 31 +++++++++++ usegalaxy.cz/get_data.yml | 2 + usegalaxy.cz/get_data.yml.lock | 8 +++ usegalaxy.cz/graph_display_data.yml.lock | 1 + usegalaxy.cz/imaging.yml | 14 +++++ usegalaxy.cz/imaging.yml.lock | 45 +++++++++++++++ usegalaxy.cz/mapping.yml.lock | 2 + usegalaxy.cz/metabolomics.yml | 20 +++++++ usegalaxy.cz/metabolomics.yml.lock | 61 +++++++++++++++++++++ usegalaxy.cz/metagenomic_analysis.yml | 10 ++++ usegalaxy.cz/metagenomic_analysis.yml.lock | 33 +++++++++++ usegalaxy.cz/multiple_alignments.yml | 2 + usegalaxy.cz/multiple_alignments.yml.lock | 6 ++ usegalaxy.cz/nanopore.yml.lock | 3 + usegalaxy.cz/picard.yml.lock | 1 + usegalaxy.cz/proteomics.yml.lock | 1 + usegalaxy.cz/quality_control.yml.lock | 2 + usegalaxy.cz/rna_analysis.yml | 2 + usegalaxy.cz/rna_analysis.yml.lock | 6 ++ usegalaxy.cz/sam_bam.yml.lock | 7 +++ usegalaxy.cz/single_cell.yml.lock | 8 +++ usegalaxy.cz/text_manipulation.yml.lock | 9 +-- usegalaxy.cz/transcriptomics.yml | 6 ++ usegalaxy.cz/transcriptomics.yml.lock | 19 +++++++ usegalaxy.cz/variant_calling.yml.lock | 10 ++++ usegalaxy.cz/virology.yml.lock | 2 + 38 files changed, 487 insertions(+), 6 deletions(-) create mode 100644 usegalaxy.cz/transcriptomics.yml create mode 100644 usegalaxy.cz/transcriptomics.yml.lock diff --git a/usegalaxy.cz/annotation.yml b/usegalaxy.cz/annotation.yml index 8c4f63c..8e7613a 100644 --- a/usegalaxy.cz/annotation.yml +++ b/usegalaxy.cz/annotation.yml @@ -258,3 +258,19 @@ tools: owner: iuc - name: funannotate_sort owner: iuc +- name: staramr + owner: iuc +- name: amrfinderplus + owner: iuc +- name: prodigal + owner: iuc +- name: argnorm + owner: iuc +- name: mmseqs2_taxonomy_assignment + owner: iuc +- name: compleasm + owner: iuc +- name: ncbi_fcs_adaptor + owner: richard-burhans +- name: omark + owner: iuc diff --git a/usegalaxy.cz/annotation.yml.lock b/usegalaxy.cz/annotation.yml.lock index 28569bc..3b4d0e8 100644 --- a/usegalaxy.cz/annotation.yml.lock +++ b/usegalaxy.cz/annotation.yml.lock @@ -33,6 +33,7 @@ tools: - name: busco owner: iuc revisions: + - 2babe6d5c561 - 4e70d88adf2f - 94170eee0ad8 - bb935709506a @@ -905,3 +906,52 @@ tools: - d77fdcca400e tool_panel_section_id: annotation tool_panel_section_label: Annotation +- name: staramr + owner: iuc + revisions: + - 6d5c8a6ceea0 + - eaa563bd535a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: amrfinderplus + owner: iuc + revisions: + - 7844dbe4f8e2 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: prodigal + owner: iuc + revisions: + - 91791b6ecd38 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: argnorm + owner: iuc + revisions: + - d8e95a03321a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: mmseqs2_taxonomy_assignment + owner: iuc + revisions: + - 876d26806584 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: compleasm + owner: iuc + revisions: + - fc7334661489 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: ncbi_fcs_adaptor + owner: richard-burhans + revisions: + - d55ad8533d58 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: omark + owner: iuc + revisions: + - 0291e0e81551 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation diff --git a/usegalaxy.cz/assembly.yml b/usegalaxy.cz/assembly.yml index f551e9c..01f7b99 100644 --- a/usegalaxy.cz/assembly.yml +++ b/usegalaxy.cz/assembly.yml @@ -160,3 +160,15 @@ tools: owner: bgruening - name: nextdenovo owner: bgruening +- name: meryl_count_kmers + owner: iuc +- name: meryl_groups_kmers + owner: iuc +- name: meryl_histogram_kmers + owner: iuc +- name: pretext_graph + owner: iuc +- name: pairtools_parse + owner: iuc +- name: pairtools_dedup + owner: iuc diff --git a/usegalaxy.cz/assembly.yml.lock b/usegalaxy.cz/assembly.yml.lock index d85870d..5aa07b9 100644 --- a/usegalaxy.cz/assembly.yml.lock +++ b/usegalaxy.cz/assembly.yml.lock @@ -230,6 +230,7 @@ tools: - aa39b19ca11e - cd06929b224b - d865b62f501c + - e100a765370e tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: minia @@ -615,3 +616,43 @@ tools: - 733eab97b979 tool_panel_section_id: assembly tool_panel_section_label: Assembly +- name: meryl_count_kmers + owner: iuc + revisions: + - bb6774c6aeaf + - e893b7452150 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: meryl_groups_kmers + owner: iuc + revisions: + - c4758f3bf36e + - cc8029eca6e9 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: meryl_histogram_kmers + owner: iuc + revisions: + - 9a0227fa7521 + - fa86bf923473 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pretext_graph + owner: iuc + revisions: + - 36ce83a739f2 + - 408ece2e4647 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pairtools_parse + owner: iuc + revisions: + - a5876cca7b05 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pairtools_dedup + owner: iuc + revisions: + - 3d1d241ceff2 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly diff --git a/usegalaxy.cz/bed.yml.lock b/usegalaxy.cz/bed.yml.lock index 914bb9e..cd46929 100644 --- a/usegalaxy.cz/bed.yml.lock +++ b/usegalaxy.cz/bed.yml.lock @@ -9,6 +9,7 @@ tools: - 0a5c785ac6db - 2892111d91f8 - 589e7e57fd6d + - 64e2edfe7a2c - 87ee588b3d45 - a1a923cd89e8 - a68aa6c1204a diff --git a/usegalaxy.cz/chemicaltoolbox.yml b/usegalaxy.cz/chemicaltoolbox.yml index d1c0dfd..299e8d6 100644 --- a/usegalaxy.cz/chemicaltoolbox.yml +++ b/usegalaxy.cz/chemicaltoolbox.yml @@ -246,3 +246,9 @@ tools: owner: chemteam - name: gmx_rmsf owner: chemteam +- name: qcxms_neutral_run + owner: recetox +- name: qcxms_production_run + owner: recetox +- name: qcxms_getres + owner: recetox diff --git a/usegalaxy.cz/chemicaltoolbox.yml.lock b/usegalaxy.cz/chemicaltoolbox.yml.lock index e254ce8..12c677a 100644 --- a/usegalaxy.cz/chemicaltoolbox.yml.lock +++ b/usegalaxy.cz/chemicaltoolbox.yml.lock @@ -6,6 +6,7 @@ tools: owner: chemteam revisions: - 095ad4d096d1 + - a0c154146234 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: chembl @@ -17,6 +18,7 @@ tools: - name: ambertools_antechamber owner: chemteam revisions: + - 4fff93efc0f9 - 8a839e6a1e3e tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox @@ -96,6 +98,7 @@ tools: owner: chemteam revisions: - 070e3ecc3fda + - 1d4dd4f908d4 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: openbabel_subsearch @@ -257,6 +260,7 @@ tools: owner: bgruening revisions: - 67ee76f0e497 + - bbbf5fb356dd tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: sdf_to_tab @@ -361,6 +365,7 @@ tools: owner: bgruening revisions: - 0993ac4f4a23 + - a1c53f0533b0 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: qed @@ -542,6 +547,7 @@ tools: - name: gmx_merge_topology_files owner: chemteam revisions: + - 9389cd867cf2 - bc31d02be922 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox @@ -814,3 +820,21 @@ tools: - f261fded9631 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox +- name: qcxms_neutral_run + owner: recetox + revisions: + - 475bbef634d4 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qcxms_production_run + owner: recetox + revisions: + - cbe34f060712 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qcxms_getres + owner: recetox + revisions: + - 0109f244d25a + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox diff --git a/usegalaxy.cz/collection_operations.yml.lock b/usegalaxy.cz/collection_operations.yml.lock index 7692ed4..94d1a97 100644 --- a/usegalaxy.cz/collection_operations.yml.lock +++ b/usegalaxy.cz/collection_operations.yml.lock @@ -27,12 +27,14 @@ tools: - 2ddc36385d7a - 6cbe2f30c2d7 - 750c1684d47c + - baabc30154cd tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations - name: collapse_collections owner: nml revisions: - 49bd84e136c7 + - 830961c48e42 - 90981f86000f tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations diff --git a/usegalaxy.cz/convert_formats.yml b/usegalaxy.cz/convert_formats.yml index 6b280aa..aee18bd 100644 --- a/usegalaxy.cz/convert_formats.yml +++ b/usegalaxy.cz/convert_formats.yml @@ -80,3 +80,7 @@ tools: owner: iuc - name: xmlstarlet owner: ecology +- name: tooldistillator + owner: iuc +- name: tooldistillator_summarize + owner: iuc diff --git a/usegalaxy.cz/convert_formats.yml.lock b/usegalaxy.cz/convert_formats.yml.lock index 78027a7..0f6509b 100644 --- a/usegalaxy.cz/convert_formats.yml.lock +++ b/usegalaxy.cz/convert_formats.yml.lock @@ -293,3 +293,17 @@ tools: - 4a9ac1df3278 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats +- name: tooldistillator + owner: iuc + revisions: + - 9f1c8dc0253e + - c6b5c2975e51 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: tooldistillator_summarize + owner: iuc + revisions: + - 3d0223265277 + - f4f71128f097 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats diff --git a/usegalaxy.cz/epigenetics.yml.lock b/usegalaxy.cz/epigenetics.yml.lock index 4cc0708..e8be593 100644 --- a/usegalaxy.cz/epigenetics.yml.lock +++ b/usegalaxy.cz/epigenetics.yml.lock @@ -114,18 +114,21 @@ tools: revisions: - 3df254580b06 - c3dc51297bf8 + - ebd2a52eb245 tool_panel_section_id: epigenetics tool_panel_section_label: Epigenetics - name: cooler_csort_tabix owner: lldelisle revisions: - 026950a1853c + - 8c3cba559c99 - d56db0e1555d tool_panel_section_id: epigenetics tool_panel_section_label: Epigenetics - name: cooler_cload_tabix owner: lldelisle revisions: + - 0641e1c892c6 - 168e86e96afa - 3ff6eeca667e tool_panel_section_id: epigenetics @@ -134,6 +137,7 @@ tools: owner: lldelisle revisions: - 8f71aaf6e59d + - 8f9fe0667b89 - b387933e4d3d tool_panel_section_id: epigenetics tool_panel_section_label: Epigenetics diff --git a/usegalaxy.cz/fasta_fastq.yml b/usegalaxy.cz/fasta_fastq.yml index b6ac4b0..8f596da 100644 --- a/usegalaxy.cz/fasta_fastq.yml +++ b/usegalaxy.cz/fasta_fastq.yml @@ -168,3 +168,11 @@ tools: owner: iuc - name: prinseq owner: iuc +- name: seqkit_translate + owner: iuc +- name: ncbi_fcs_gx + owner: iuc +- name: rdeval + owner: richard-burhans +- name: mgnify_seqprep + owner: bgruening diff --git a/usegalaxy.cz/fasta_fastq.yml.lock b/usegalaxy.cz/fasta_fastq.yml.lock index 30f3c26..5f88d96 100644 --- a/usegalaxy.cz/fasta_fastq.yml.lock +++ b/usegalaxy.cz/fasta_fastq.yml.lock @@ -6,6 +6,7 @@ tools: owner: lparsons revisions: - 135b80fb1ac2 + - 5eb7e84243f2 - 80766b36005d - 8c0175e03cee - 8e264b67a8c0 @@ -259,6 +260,9 @@ tools: - 281054a26e41 - 480ddbd12a03 - 65b93b623c77 + - a626e8c0e1ba + - c59d48774d03 + - dbf9c561ef29 - e25816738ef3 - f875da9d433c tool_panel_section_id: fasta_fastq @@ -272,6 +276,7 @@ tools: - name: fasta_to_tabular owner: devteam revisions: + - 7e801ab2b70e - e7ed3c310b74 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -643,3 +648,29 @@ tools: - 654b3a274ed5 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ +- name: seqkit_translate + owner: iuc + revisions: + - 0e0b003c711f + - c669e8550c46 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 5fe428757fab + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: rdeval + owner: richard-burhans + revisions: + - 37d67c252fed + - aef1eea2058c + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: mgnify_seqprep + owner: bgruening + revisions: + - 76ea9d4604bc + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized diff --git a/usegalaxy.cz/get_data.yml b/usegalaxy.cz/get_data.yml index a8f05a0..e603b75 100644 --- a/usegalaxy.cz/get_data.yml +++ b/usegalaxy.cz/get_data.yml @@ -60,3 +60,5 @@ tools: owner: iuc - name: ega_download_streamer owner: yhoogstrate +- name: fastq_dl + owner: iuc diff --git a/usegalaxy.cz/get_data.yml.lock b/usegalaxy.cz/get_data.yml.lock index b6fe483..b8c75ec 100644 --- a/usegalaxy.cz/get_data.yml.lock +++ b/usegalaxy.cz/get_data.yml.lock @@ -31,6 +31,7 @@ tools: - 26b7446bb17e - 494b2ec08162 - 4df8de2d0e48 + - 516a54ddf218 - 653e89d73fc4 - 69ebb7f46e45 - 6ea73833cf67 @@ -231,3 +232,10 @@ tools: - 3e2cccf08053 tool_panel_section_id: get_data tool_panel_section_label: Get Data +- name: fastq_dl + owner: iuc + revisions: + - 3f1ee30e39e9 + - 41635d6d4738 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data diff --git a/usegalaxy.cz/graph_display_data.yml.lock b/usegalaxy.cz/graph_display_data.yml.lock index be40208..d4921d7 100644 --- a/usegalaxy.cz/graph_display_data.yml.lock +++ b/usegalaxy.cz/graph_display_data.yml.lock @@ -159,6 +159,7 @@ tools: owner: iuc revisions: - 11c344627e52 + - 2f557f6abbfb - 5e08a1e22dbc - 83c573f2e73c - cfb0595f9842 diff --git a/usegalaxy.cz/imaging.yml b/usegalaxy.cz/imaging.yml index 0ba4a47..53fd037 100644 --- a/usegalaxy.cz/imaging.yml +++ b/usegalaxy.cz/imaging.yml @@ -196,3 +196,17 @@ tools: owner: goeckslab - name: mesmer owner: goeckslab +- name: squidpy_scatter + owner: goeckslab +- name: squidpy_spatial + owner: goeckslab +- name: imagemagick_image_montage + owner: bgruening +- name: scimap_mcmicro_to_anndata + owner: goeckslab +- name: scimap_phenotyping + owner: goeckslab +- name: backsub + owner: goeckslab +- name: scimap_plotting + owner: goeckslab diff --git a/usegalaxy.cz/imaging.yml.lock b/usegalaxy.cz/imaging.yml.lock index dcc7cb9..da7f698 100644 --- a/usegalaxy.cz/imaging.yml.lock +++ b/usegalaxy.cz/imaging.yml.lock @@ -732,3 +732,48 @@ tools: - 53240d7c1fc5 tool_panel_section_id: imaging tool_panel_section_label: Imaging +- name: squidpy_scatter + owner: goeckslab + revisions: + - b84c324b58bd + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: squidpy_spatial + owner: goeckslab + revisions: + - 2a5036c29889 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: imagemagick_image_montage + owner: bgruening + revisions: + - 506a90ab5581 + - 65703c06c1f6 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: scimap_mcmicro_to_anndata + owner: goeckslab + revisions: + - 49c178651194 + - b1ead1b7e0aa + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: scimap_phenotyping + owner: goeckslab + revisions: + - 37dc4f51e827 + - 88fca6e905be + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: backsub + owner: goeckslab + revisions: + - bf9f98a7f936 + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: scimap_plotting + owner: goeckslab + revisions: + - 05a8d9dea3df + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized diff --git a/usegalaxy.cz/mapping.yml.lock b/usegalaxy.cz/mapping.yml.lock index c546c98..d7c39a0 100644 --- a/usegalaxy.cz/mapping.yml.lock +++ b/usegalaxy.cz/mapping.yml.lock @@ -7,8 +7,10 @@ tools: revisions: - 11a0d50a54e6 - 539de907fd99 + - 5cc34c3f440d - 66367287b4e6 - 6945cd53bd2d + - 8c6cd2650d1f - be1d967337e4 tool_panel_section_id: mapping tool_panel_section_label: Mapping diff --git a/usegalaxy.cz/metabolomics.yml b/usegalaxy.cz/metabolomics.yml index 503b0f9..e0ce0c0 100644 --- a/usegalaxy.cz/metabolomics.yml +++ b/usegalaxy.cz/metabolomics.yml @@ -200,3 +200,23 @@ tools: owner: iuc - name: dimet_timecourse_analysis owner: iuc +- name: mfassignr_kmdnoise + owner: recetox +- name: mfassignr_histnoise + owner: recetox +- name: mfassignr_snplot + owner: recetox +- name: mfassignr_isofiltr + owner: recetox +- name: mfassignr_mfassigncho + owner: recetox +- name: mfassignr_recallist + owner: recetox +- name: mfassignr_findrecalseries + owner: recetox +- name: mfassignr_recal + owner: recetox +- name: mfassignr_mfassign + owner: recetox +- name: table_pandas_rename_column + owner: recetox diff --git a/usegalaxy.cz/metabolomics.yml.lock b/usegalaxy.cz/metabolomics.yml.lock index bc2ec59..956abf1 100644 --- a/usegalaxy.cz/metabolomics.yml.lock +++ b/usegalaxy.cz/metabolomics.yml.lock @@ -749,3 +749,64 @@ tools: - cb8c4ae59da9 tool_panel_section_id: metabolomics tool_panel_section_label: Metabolomics +- name: mfassignr_kmdnoise + owner: recetox + revisions: + - a7a823839ae3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_histnoise + owner: recetox + revisions: + - 9654573e6889 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_snplot + owner: recetox + revisions: + - f19c0631b9e5 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_isofiltr + owner: recetox + revisions: + - 1c199c3d5993 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_mfassigncho + owner: recetox + revisions: + - da64d663694b + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_recallist + owner: recetox + revisions: + - 6c7b17d38a1d + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_findrecalseries + owner: recetox + revisions: + - 1b4881c150cc + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_recal + owner: recetox + revisions: + - cfcf45ba58be + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_mfassign + owner: recetox + revisions: + - 22c80f584bb1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: table_pandas_rename_column + owner: recetox + revisions: + - 3f54cd56a65e + - 8537763e4713 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics diff --git a/usegalaxy.cz/metagenomic_analysis.yml b/usegalaxy.cz/metagenomic_analysis.yml index 98cc80e..3e32bfa 100644 --- a/usegalaxy.cz/metagenomic_analysis.yml +++ b/usegalaxy.cz/metagenomic_analysis.yml @@ -338,3 +338,13 @@ tools: owner: bebatut - name: mapseq owner: iuc +- name: checkm2 + owner: iuc +- name: binette + owner: iuc +- name: gtdbtk_classify_wf + owner: iuc +- name: mash_paste + owner: iuc +- name: mash_dist + owner: iuc diff --git a/usegalaxy.cz/metagenomic_analysis.yml.lock b/usegalaxy.cz/metagenomic_analysis.yml.lock index b2a7cff..6143ee6 100644 --- a/usegalaxy.cz/metagenomic_analysis.yml.lock +++ b/usegalaxy.cz/metagenomic_analysis.yml.lock @@ -120,6 +120,7 @@ tools: - name: kraken2 owner: iuc revisions: + - 20e2f64aa1fe - 241a78eb2935 - cdee7158adf3 - e150ae930235 @@ -1343,3 +1344,35 @@ tools: - f1d1dafc836d tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis +- name: checkm2 + owner: iuc + revisions: + - 304ac5b49dea + - 66acaec9f386 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: binette + owner: iuc + revisions: + - 37ab2cfedac4 + - 9053a39d7994 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: gtdbtk_classify_wf + owner: iuc + revisions: + - 53a019316350 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash_paste + owner: iuc + revisions: + - e0c0fda064eb + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash_dist + owner: iuc + revisions: + - c932095af671 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis diff --git a/usegalaxy.cz/multiple_alignments.yml b/usegalaxy.cz/multiple_alignments.yml index 53198ae..499414b 100644 --- a/usegalaxy.cz/multiple_alignments.yml +++ b/usegalaxy.cz/multiple_alignments.yml @@ -42,3 +42,5 @@ tools: owner: rnateam - name: cd_hit owner: iuc +- name: mmseqs2_easy_linclust_clustering + owner: iuc diff --git a/usegalaxy.cz/multiple_alignments.yml.lock b/usegalaxy.cz/multiple_alignments.yml.lock index 4284c57..222f247 100644 --- a/usegalaxy.cz/multiple_alignments.yml.lock +++ b/usegalaxy.cz/multiple_alignments.yml.lock @@ -145,3 +145,9 @@ tools: - 7807800a3d03 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments +- name: mmseqs2_easy_linclust_clustering + owner: iuc + revisions: + - b174c3405549 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments diff --git a/usegalaxy.cz/nanopore.yml.lock b/usegalaxy.cz/nanopore.yml.lock index b83df68..1703e3c 100644 --- a/usegalaxy.cz/nanopore.yml.lock +++ b/usegalaxy.cz/nanopore.yml.lock @@ -5,6 +5,7 @@ tools: - name: medaka_variant owner: iuc revisions: + - 0f5f4a208660 - 16fc9856b20a - eb746fa6f514 - ec699520444c @@ -46,6 +47,7 @@ tools: owner: iuc revisions: - 18505fe2bdb1 + - db25ec99c3ea - fc1f197b33ec tool_panel_section_id: nanopore tool_panel_section_label: Nanopore @@ -61,6 +63,7 @@ tools: - 025139097795 - 0f1c34698076 - 2a9afed42353 + - a02b8b3f5a0c - a3c4fe6f49ab tool_panel_section_id: nanopore tool_panel_section_label: Nanopore diff --git a/usegalaxy.cz/picard.yml.lock b/usegalaxy.cz/picard.yml.lock index f4ed0e8..4c90e19 100644 --- a/usegalaxy.cz/picard.yml.lock +++ b/usegalaxy.cz/picard.yml.lock @@ -9,6 +9,7 @@ tools: - 3f254c5ced1d - 585027e65f3b - 881d7645d1bf + - a1f0b3f4b781 - ab1f60c26526 - b502c227b5e6 - f9242e01365a diff --git a/usegalaxy.cz/proteomics.yml.lock b/usegalaxy.cz/proteomics.yml.lock index 253701f..fd308ad 100644 --- a/usegalaxy.cz/proteomics.yml.lock +++ b/usegalaxy.cz/proteomics.yml.lock @@ -1770,6 +1770,7 @@ tools: owner: galaxyp revisions: - 3ec27b4cee7c + - a6ff76e057fd tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: rawtools diff --git a/usegalaxy.cz/quality_control.yml.lock b/usegalaxy.cz/quality_control.yml.lock index 6edb462..a7a7eca 100644 --- a/usegalaxy.cz/quality_control.yml.lock +++ b/usegalaxy.cz/quality_control.yml.lock @@ -11,6 +11,7 @@ tools: - 5e33b465d8d5 - 75c93c70d094 - 9a913cdee30e + - a7e081ceb76a - abfd8a6544d7 - b2f1f75d49c4 - bf675f34b056 @@ -18,6 +19,7 @@ tools: - c1a4b5f3b432 - e4574a4d09d8 - e4dd4c0622f6 + - f7e2f1eb3a16 tool_panel_section_id: quality_control tool_panel_section_label: Quality Control - name: fastq_info diff --git a/usegalaxy.cz/rna_analysis.yml b/usegalaxy.cz/rna_analysis.yml index fd42d18..7a4899e 100644 --- a/usegalaxy.cz/rna_analysis.yml +++ b/usegalaxy.cz/rna_analysis.yml @@ -292,3 +292,5 @@ tools: owner: rnateam - name: psiclass owner: iuc +- name: brew3r_r + owner: iuc diff --git a/usegalaxy.cz/rna_analysis.yml.lock b/usegalaxy.cz/rna_analysis.yml.lock index 3ba8bfb..6448540 100644 --- a/usegalaxy.cz/rna_analysis.yml.lock +++ b/usegalaxy.cz/rna_analysis.yml.lock @@ -976,3 +976,9 @@ tools: - 1b690aa060f6 tool_panel_section_id: rna_analysis tool_panel_section_label: RNA Analysis +- name: brew3r_r + owner: iuc + revisions: + - d3b0390f325f + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis diff --git a/usegalaxy.cz/sam_bam.yml.lock b/usegalaxy.cz/sam_bam.yml.lock index c0721be..f6c08e1 100644 --- a/usegalaxy.cz/sam_bam.yml.lock +++ b/usegalaxy.cz/sam_bam.yml.lock @@ -90,10 +90,13 @@ tools: - name: samtools_view owner: iuc revisions: + - 0dbf49c414ae - 32dc5f781059 - 48bbbcb692ce - 5826298f6a73 - 5ec526530725 + - bf328cec6a42 + - c370440f901e tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM - name: samtools_reheader @@ -109,6 +112,7 @@ tools: - name: qualimap_bamqc owner: iuc revisions: + - 19ece8afbaab - 30a201c9c310 - 4a89c6f84425 tool_panel_section_id: sam_bam @@ -158,6 +162,7 @@ tools: owner: iuc revisions: - 491037bfc0d2 + - 66e23b11feae - 9038311ed624 - b3d99709fe1a - b906586a6596 @@ -175,6 +180,8 @@ tools: - name: samtools_stats owner: devteam revisions: + - 145f6d74ff5e + - 1cc79f49b8d5 - 1ed8ed887035 - 3a0efe14891f - 541082d03bef diff --git a/usegalaxy.cz/single_cell.yml.lock b/usegalaxy.cz/single_cell.yml.lock index 2da26a3..a13cb97 100644 --- a/usegalaxy.cz/single_cell.yml.lock +++ b/usegalaxy.cz/single_cell.yml.lock @@ -21,6 +21,7 @@ tools: revisions: - 13cf83ced60c - 923dcc644832 + - d330b3082107 - fb9e030ffae4 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -36,6 +37,7 @@ tools: owner: iuc revisions: - 3d748954434b + - 7e8c677a7b71 - be1fdce914c6 - d1e49c3c0aa2 tool_panel_section_id: single_cell @@ -43,6 +45,7 @@ tools: - name: anndata_inspect owner: iuc revisions: + - 0bf7fddf90c7 - 33c0081e16c6 - afe044e6bc93 - ee98d611afc6 @@ -91,6 +94,7 @@ tools: revisions: - 5813f9920877 - 5b3c1679d29b + - 8cb783c81905 - b409c2486353 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell @@ -107,12 +111,14 @@ tools: revisions: - 4766556db52c - 4bda4412b8c2 + - 56c0d4acef02 - ab55fe8030b6 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell - name: scanpy_plot owner: iuc revisions: + - 0185bd174ea0 - 5a5468c0d26f - 62acdd96d4a0 - aa0c474463c2 @@ -122,6 +128,7 @@ tools: owner: iuc revisions: - 458d4ab0f894 + - 9fb627495ec2 - bf2017df9837 - c5541bfb8feb tool_panel_section_id: single_cell @@ -137,6 +144,7 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - 38db3fef7aad - 8983e7a04ba7 - a84a73471be7 - aaa5da8e73a9 diff --git a/usegalaxy.cz/text_manipulation.yml.lock b/usegalaxy.cz/text_manipulation.yml.lock index 158dc13..62baa1a 100644 --- a/usegalaxy.cz/text_manipulation.yml.lock +++ b/usegalaxy.cz/text_manipulation.yml.lock @@ -35,6 +35,8 @@ tools: - name: column_maker owner: devteam revisions: + - 02026300aa45 + - 427903d47026 - 626658afe4cb - 6595517c2dd8 - 9cd341095afd @@ -109,6 +111,7 @@ tools: - 86755160afbf - c41d78ae5fee - d698c222f354 + - ddf54b12c295 - f46f0e4f75c4 - fbf99087e067 tool_panel_section_id: text_manipulation @@ -266,12 +269,6 @@ tools: - 5b1b635232ed tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation -- name: jq - owner: iuc - revisions: - - 5ff75eb1a893 - tool_panel_section_id: text_manipulation - tool_panel_section_label: Text Manipulation - name: tesseract owner: iuc revisions: diff --git a/usegalaxy.cz/transcriptomics.yml b/usegalaxy.cz/transcriptomics.yml new file mode 100644 index 0000000..16e60cd --- /dev/null +++ b/usegalaxy.cz/transcriptomics.yml @@ -0,0 +1,6 @@ +tool_panel_section_label: CellTypeScan +tools: +- name: decoupler_pseudobulk + owner: ebi-gxa +- name: anndata_ops + owner: ebi-gxa diff --git a/usegalaxy.cz/transcriptomics.yml.lock b/usegalaxy.cz/transcriptomics.yml.lock new file mode 100644 index 0000000..01c728a --- /dev/null +++ b/usegalaxy.cz/transcriptomics.yml.lock @@ -0,0 +1,19 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: CellTypeScan +tools: +- name: decoupler_pseudobulk + owner: ebi-gxa + revisions: + - 2557d7869e78 + - ef054892d47f + tool_panel_section_id: transcriptomics + tool_panel_section_label: Transcriptomics +- name: anndata_ops + owner: ebi-gxa + revisions: + - 7ef2403a250d + - a4774b7b2e85 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy diff --git a/usegalaxy.cz/variant_calling.yml.lock b/usegalaxy.cz/variant_calling.yml.lock index 8566bd7..be4fce7 100644 --- a/usegalaxy.cz/variant_calling.yml.lock +++ b/usegalaxy.cz/variant_calling.yml.lock @@ -159,6 +159,7 @@ tools: revisions: - 09d6806c609e - 2b3e65a4252f + - 2e497a770bca - 5fab4f81391d - b04635ebfab0 tool_panel_section_id: variant_calling @@ -179,6 +180,7 @@ tools: owner: iuc revisions: - 7dfca164d2e3 + - 950d1d49d678 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_call @@ -186,6 +188,7 @@ tools: revisions: - 4805fe3d8fda - b11e8e9c23bf + - e1461b5c52a0 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: plink @@ -248,6 +251,7 @@ tools: owner: iuc revisions: - aa35ee7f3ab2 + - af7e416d8176 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_alnqual @@ -259,6 +263,8 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - 354b534eeab7 + - 426d707dfc47 - 971e07ca4456 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling @@ -529,6 +535,7 @@ tools: - 85dc96ebc770 - a5937157062f - e698621cca1f + - ef2c525bd8cd tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: snpeff @@ -537,6 +544,8 @@ tools: - 3aae4f16ac9e - 5b80f544c67f - 5c7b70713fb5 + - 6322be79bd8e + - 74aebe30fb52 - c7275bd8b4d6 - e8adfc4c0a6b tool_panel_section_id: variant_calling @@ -815,6 +824,7 @@ tools: - 06eaadeffb7d - 2c372041ed8c - 3f62d4939d54 + - 403553ae19f6 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: beagle diff --git a/usegalaxy.cz/virology.yml.lock b/usegalaxy.cz/virology.yml.lock index b1b593a..9f3fc0f 100644 --- a/usegalaxy.cz/virology.yml.lock +++ b/usegalaxy.cz/virology.yml.lock @@ -8,6 +8,7 @@ tools: - 0893a1dbb807 - 6606a8c97889 - 7bd020da0ce5 + - c092052ed673 - f0cc9cf99407 tool_panel_section_id: virology tool_panel_section_label: Virology @@ -38,6 +39,7 @@ tools: - name: ivar_variants owner: iuc revisions: + - 045d6d00f606 - 194e3ceee923 - 1ef68546d37f - 5e5dfc9e71e2