From bf4a6532b6b84769acd0a5708f5b4d06bdbd9da3 Mon Sep 17 00:00:00 2001 From: Delphine Lariviere Date: Sat, 29 Jun 2024 16:00:22 +0200 Subject: [PATCH] add single cell tools --- usegalaxy.org/hca-scanpy.yml | 16 ++ usegalaxy.org/hca-scanpy.yml.lock | 47 ++++ usegalaxy.org/hicexplorer.yml | 120 ++++++++++ usegalaxy.org/hicexplorer.yml.lock | 359 +++++++++++++++++++++++++++++ usegalaxy.org/import.yml | 8 + usegalaxy.org/import.yml.lock | 23 ++ usegalaxy.org/multiomics.yml | 4 + usegalaxy.org/multiomics.yml.lock | 11 + usegalaxy.org/sccaf.yml | 10 + usegalaxy.org/sccaf.yml.lock | 29 +++ usegalaxy.org/seurat.yml | 28 +++ usegalaxy.org/seurat.yml.lock | 83 +++++++ usegalaxy.org/single_cell.yml | 10 + usegalaxy.org/single_cell.yml.lock | 30 +++ usegalaxy.org/spatial.yml | 14 ++ usegalaxy.org/spatial.yml.lock | 41 ++++ 16 files changed, 833 insertions(+) create mode 100644 usegalaxy.org/hca-scanpy.yml create mode 100644 usegalaxy.org/hca-scanpy.yml.lock create mode 100644 usegalaxy.org/hicexplorer.yml create mode 100644 usegalaxy.org/hicexplorer.yml.lock create mode 100644 usegalaxy.org/import.yml create mode 100644 usegalaxy.org/import.yml.lock create mode 100644 usegalaxy.org/multiomics.yml create mode 100644 usegalaxy.org/multiomics.yml.lock create mode 100644 usegalaxy.org/sccaf.yml create mode 100644 usegalaxy.org/sccaf.yml.lock create mode 100644 usegalaxy.org/seurat.yml create mode 100644 usegalaxy.org/seurat.yml.lock create mode 100644 usegalaxy.org/spatial.yml create mode 100644 usegalaxy.org/spatial.yml.lock diff --git a/usegalaxy.org/hca-scanpy.yml b/usegalaxy.org/hca-scanpy.yml new file mode 100644 index 00000000..30e12240 --- /dev/null +++ b/usegalaxy.org/hca-scanpy.yml @@ -0,0 +1,16 @@ +tool_panel_section_label: HCA-Scanpy +tools: +- name: seurat_plot + owner: ebi-gxa +- name: scanpy_integrate_bbknn + owner: ebi-gxa +- name: scanpy_integrate_combat + owner: ebi-gxa +- name: scanpy_integrate_mnn + owner: ebi-gxa +- name: scanpy_plot_scrublet + owner: ebi-gxa +- name: scanpy_multiplet_scrublet + owner: ebi-gxa +- name: seurat_run_umap + owner: ebi-gxa diff --git a/usegalaxy.org/hca-scanpy.yml.lock b/usegalaxy.org/hca-scanpy.yml.lock new file mode 100644 index 00000000..62bc2659 --- /dev/null +++ b/usegalaxy.org/hca-scanpy.yml.lock @@ -0,0 +1,47 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: HCA-Scanpy +tools: +- name: seurat_plot + owner: ebi-gxa + revisions: + - 95d79f1134f0 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_bbknn + owner: ebi-gxa + revisions: + - c9da9192eee5 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_combat + owner: ebi-gxa + revisions: + - 3c47bc560688 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_integrate_mnn + owner: ebi-gxa + revisions: + - ff6decc0f432 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_plot_scrublet + owner: ebi-gxa + revisions: + - 6f5509cf3176 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: scanpy_multiplet_scrublet + owner: ebi-gxa + revisions: + - 53ce0e336840 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy +- name: seurat_run_umap + owner: ebi-gxa + revisions: + - b9424c715a0d + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy diff --git a/usegalaxy.org/hicexplorer.yml b/usegalaxy.org/hicexplorer.yml new file mode 100644 index 00000000..7c94a0de --- /dev/null +++ b/usegalaxy.org/hicexplorer.yml @@ -0,0 +1,120 @@ +tool_panel_section_label: HiCExplorer +tools: +- name: hicexplorer_chicaggregatestatistic + owner: bgruening +- name: hicexplorer_chicdifferentialtest + owner: bgruening +- name: hicexplorer_chicexportdata + owner: bgruening +- name: hicexplorer_chicplotviewpoint + owner: bgruening +- name: hicexplorer_chicqualitycontrol + owner: bgruening +- name: hicexplorer_chicsignificantinteractions + owner: bgruening +- name: hicexplorer_chicviewpoint + owner: bgruening +- name: hicexplorer_chicqualitycontrol + owner: bgruening +- name: hicexplorer_chicsignificantinteractions + owner: bgruening +- name: hicexplorer_chicviewpoint + owner: bgruening +- name: hicexplorer_chicviewpointbackgroundmodel + owner: bgruening +- name: hicexplorer_hicadjustmatrix + owner: bgruening +- name: hicexplorer_hicaggregatecontacts + owner: bgruening +- name: hicexplorer_hicaverageregions + owner: bgruening +- name: hicexplorer_hicbuildmatrix + owner: bgruening +- name: hicexplorer_hiccomparematrices + owner: bgruening +- name: hicexplorer_hiccompartmentspolarization + owner: bgruening +- name: hicexplorer_hicconvertformat + owner: bgruening +- name: hicexplorer_hiccorrectmatrix + owner: bgruening +- name: hicexplorer_hiccorrelate + owner: bgruening +- name: hicexplorer_hicdetectloops + owner: bgruening +- name: hicexplorer_hicdifferentialtad + owner: bgruening +- name: hicexplorer_hicfindrestrictionsites + owner: bgruening +- name: hicexplorer_hicfindtads + owner: bgruening +- name: hicexplorer_hichyperoptdetectloops + owner: bgruening +- name: hicexplorer_hicinfo + owner: bgruening +- name: hicexplorer_hicinterintratad + owner: bgruening +- name: hicexplorer_hicmergedomains + owner: bgruening +- name: hicexplorer_hicmergeloops + owner: bgruening +- name: hicexplorer_hicmergematrixbins + owner: bgruening +- name: hicexplorer_hicnormalize + owner: bgruening +- name: hicexplorer_hicpca + owner: bgruening +- name: hicexplorer_hicplotaverageregions + owner: bgruening +- name: hicexplorer_hicplotdistvscounts + owner: bgruening +- name: hicexplorer_hicplotmatrix + owner: bgruening +- name: hicexplorer_hicplotsvl + owner: bgruening +- name: hicexplorer_hicplotviewpoint + owner: bgruening +- name: hicexplorer_hicquickqc + owner: bgruening +- name: hicexplorer_hicsummatrices + owner: bgruening +- name: hicexplorer_hictadclassifier + owner: bgruening +- name: hicexplorer_hictraintadclassifier + owner: bgruening +- name: hicexplorer_hictransform + owner: bgruening +- name: hicexplorer_hicvalidatelocations + owner: bgruening +- name: schicexplorer_schicadjustmatrix + owner: iuc +- name: schicexplorer_schiccluster + owner: iuc +- name: schicexplorer_schicclustercompartments + owner: iuc +- name: schicexplorer_schicclusterminhash + owner: iuc +- name: schicexplorer_schicclustersvl + owner: iuc +- name: schicexplorer_schicconsensusmatrices + owner: iuc +- name: schicexplorer_schiccorrectmatrices + owner: iuc +- name: schicexplorer_schiccreatebulkmatrix + owner: iuc +- name: schicexplorer_schicdemultiplex + owner: iuc +- name: schicexplorer_schicinfo + owner: iuc +- name: schicexplorer_schicmergematrixbins + owner: iuc +- name: schicexplorer_schicmergetoscool + owner: iuc +- name: schicexplorer_schicnormalize + owner: iuc +- name: schicexplorer_schicplotclusterprofiles + owner: iuc +- name: schicexplorer_schicplotconsensusmatrices + owner: iuc +- name: schicexplorer_schicqualitycontrol + owner: iuc diff --git a/usegalaxy.org/hicexplorer.yml.lock b/usegalaxy.org/hicexplorer.yml.lock new file mode 100644 index 00000000..a86a55c1 --- /dev/null +++ b/usegalaxy.org/hicexplorer.yml.lock @@ -0,0 +1,359 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: HiCExplorer +tools: +- name: hicexplorer_chicaggregatestatistic + owner: bgruening + revisions: + - 01c37e54e86e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicdifferentialtest + owner: bgruening + revisions: + - 9d42a6133690 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicexportdata + owner: bgruening + revisions: + - 23b8d6b8960c + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicplotviewpoint + owner: bgruening + revisions: + - 013e53ccc7ac + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicqualitycontrol + owner: bgruening + revisions: + - b892fa1fcaec + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicsignificantinteractions + owner: bgruening + revisions: + - 640e0e45518a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpoint + owner: bgruening + revisions: + - f881c94fb3b3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicqualitycontrol + owner: bgruening + revisions: + - b892fa1fcaec + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicsignificantinteractions + owner: bgruening + revisions: + - 640e0e45518a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpoint + owner: bgruening + revisions: + - f881c94fb3b3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_chicviewpointbackgroundmodel + owner: bgruening + revisions: + - 9d02f1819e81 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicadjustmatrix + owner: bgruening + revisions: + - 2dccb6bb0add + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicaggregatecontacts + owner: bgruening + revisions: + - f0216498a666 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicaverageregions + owner: bgruening + revisions: + - c72fa6cb8817 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicbuildmatrix + owner: bgruening + revisions: + - ed2cca6b5de4 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccomparematrices + owner: bgruening + revisions: + - 3ee5332bf57c + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccompartmentspolarization + owner: bgruening + revisions: + - 3a6a5381db36 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicconvertformat + owner: bgruening + revisions: + - c0737631eea1 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccorrectmatrix + owner: bgruening + revisions: + - ea19190ce5e0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hiccorrelate + owner: bgruening + revisions: + - 2b4d6a8dab36 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicdetectloops + owner: bgruening + revisions: + - 0410b6aada45 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicdifferentialtad + owner: bgruening + revisions: + - 77d8e0fd162a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicfindrestrictionsites + owner: bgruening + revisions: + - 6c5097f6d41e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicfindtads + owner: bgruening + revisions: + - ec4b948dc6f0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hichyperoptdetectloops + owner: bgruening + revisions: + - 7f7c6ead2d0d + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicinfo + owner: bgruening + revisions: + - e4f8fceab96a + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicinterintratad + owner: bgruening + revisions: + - 55b013e59018 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicmergedomains + owner: bgruening + revisions: + - b376ef118807 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicmergeloops + owner: bgruening + revisions: + - 1511a8ebe906 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicmergematrixbins + owner: bgruening + revisions: + - 977dc15add20 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicnormalize + owner: bgruening + revisions: + - 6d042c96aceb + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicpca + owner: bgruening + revisions: + - 77919cc3618e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicplotaverageregions + owner: bgruening + revisions: + - ea5d67ec94ab + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicplotdistvscounts + owner: bgruening + revisions: + - 6326cd29c1c3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicplotmatrix + owner: bgruening + revisions: + - b63363075c2e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicplotsvl + owner: bgruening + revisions: + - b4e780e93c91 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicplotviewpoint + owner: bgruening + revisions: + - 58de3c7c8e89 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicquickqc + owner: bgruening + revisions: + - 21d859ad4502 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicsummatrices + owner: bgruening + revisions: + - 36dfa2825a59 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hictadclassifier + owner: bgruening + revisions: + - 887d203233e5 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hictraintadclassifier + owner: bgruening + revisions: + - 1ff19476c5a5 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hictransform + owner: bgruening + revisions: + - f36828ebdc54 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: hicexplorer_hicvalidatelocations + owner: bgruening + revisions: + - 1d201e8378b3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicadjustmatrix + owner: iuc + revisions: + - 2e773e00ceb0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schiccluster + owner: iuc + revisions: + - baa3ae7ac42c + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicclustercompartments + owner: iuc + revisions: + - 54b6cef88a7f + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicclusterminhash + owner: iuc + revisions: + - 3048283ee054 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicclustersvl + owner: iuc + revisions: + - e6ec3914a076 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicconsensusmatrices + owner: iuc + revisions: + - 33b1c99cc709 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schiccorrectmatrices + owner: iuc + revisions: + - 295558e266d0 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schiccreatebulkmatrix + owner: iuc + revisions: + - acb3ed49109e + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicdemultiplex + owner: iuc + revisions: + - f224fc9af1d3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicinfo + owner: iuc + revisions: + - 41b415c410e3 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicmergematrixbins + owner: iuc + revisions: + - 47ef02546fe9 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicmergetoscool + owner: iuc + revisions: + - 70a13d0a950f + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicnormalize + owner: iuc + revisions: + - 66e96c3d3c5d + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicplotclusterprofiles + owner: iuc + revisions: + - 65f2f5d29947 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicplotconsensusmatrices + owner: iuc + revisions: + - 95b1216e1e70 + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer +- name: schicexplorer_schicqualitycontrol + owner: iuc + revisions: + - 4a841ab67e3b + tool_panel_section_id: hicexplorer + tool_panel_section_label: HiCExplorer diff --git a/usegalaxy.org/import.yml b/usegalaxy.org/import.yml new file mode 100644 index 00000000..f87138d9 --- /dev/null +++ b/usegalaxy.org/import.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: Import/manipulate sc data +tools: +- name: 10x_bamtofastq + owner: bgruening +- name: scater_read_10x_results + owner: ebi-gxa +- name: gsc_scran_normalize + owner: artbio diff --git a/usegalaxy.org/import.yml.lock b/usegalaxy.org/import.yml.lock new file mode 100644 index 00000000..8b5f8cd3 --- /dev/null +++ b/usegalaxy.org/import.yml.lock @@ -0,0 +1,23 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Import/manipulate sc data +tools: +- name: 10x_bamtofastq + owner: bgruening + revisions: + - f71fd828c126 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data +- name: scater_read_10x_results + owner: ebi-gxa + revisions: + - da3f394039b5 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data +- name: gsc_scran_normalize + owner: artbio + revisions: + - 6864acb21714 + tool_panel_section_id: import_manipulate_sc_data + tool_panel_section_label: Import/manipulate sc data diff --git a/usegalaxy.org/multiomics.yml b/usegalaxy.org/multiomics.yml new file mode 100644 index 00000000..e305aae5 --- /dev/null +++ b/usegalaxy.org/multiomics.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Multiomics +tools: +- name: episcanpy_cluster_embed + owner: iuc diff --git a/usegalaxy.org/multiomics.yml.lock b/usegalaxy.org/multiomics.yml.lock new file mode 100644 index 00000000..467ea6c6 --- /dev/null +++ b/usegalaxy.org/multiomics.yml.lock @@ -0,0 +1,11 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Multiomics +tools: +- name: episcanpy_cluster_embed + owner: iuc + revisions: + - f4713992f23a + tool_panel_section_id: multiomics + tool_panel_section_label: Multiomics diff --git a/usegalaxy.org/sccaf.yml b/usegalaxy.org/sccaf.yml new file mode 100644 index 00000000..45909169 --- /dev/null +++ b/usegalaxy.org/sccaf.yml @@ -0,0 +1,10 @@ +tool_panel_section_label: SCCAF +tools: +- name: run_sccaf + owner: ebi-gxa +- name: sccaf_asses + owner: ebi-gxa +- name: sccaf_asses_merger + owner: ebi-gxa +- name: sccaf_regress_out + owner: ebi-gxa diff --git a/usegalaxy.org/sccaf.yml.lock b/usegalaxy.org/sccaf.yml.lock new file mode 100644 index 00000000..49c80525 --- /dev/null +++ b/usegalaxy.org/sccaf.yml.lock @@ -0,0 +1,29 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: SCCAF +tools: +- name: run_sccaf + owner: ebi-gxa + revisions: + - 647d34f125bc + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_asses + owner: ebi-gxa + revisions: + - 37a4c22f600b + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_asses_merger + owner: ebi-gxa + revisions: + - 99d15ded4d5f + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF +- name: sccaf_regress_out + owner: ebi-gxa + revisions: + - 5ef0610e9f50 + tool_panel_section_id: sccaf + tool_panel_section_label: SCCAF diff --git a/usegalaxy.org/seurat.yml b/usegalaxy.org/seurat.yml new file mode 100644 index 00000000..0b95e939 --- /dev/null +++ b/usegalaxy.org/seurat.yml @@ -0,0 +1,28 @@ +tool_panel_section_label: Seurat +tools: +- name: seurat_create_seurat_object + owner: ebi-gxa +- name: seurat_export_cellbrowser + owner: ebi-gxa +- name: seurat_filter_cells + owner: ebi-gxa +- name: seurat_find_clusters + owner: ebi-gxa +- name: seurat_find_markers + owner: ebi-gxa +- name: seurat_find_neighbours + owner: ebi-gxa +- name: seurat_find_variable_genes + owner: ebi-gxa +- name: seurat_normalise_data + owner: ebi-gxa +- name: seurat_dim_plot + owner: ebi-gxa +- name: seurat_read10x + owner: ebi-gxa +- name: seurat_run_pca + owner: ebi-gxa +- name: seurat_run_tsne + owner: ebi-gxa +- name: seurat_scale_data + owner: ebi-gxa diff --git a/usegalaxy.org/seurat.yml.lock b/usegalaxy.org/seurat.yml.lock new file mode 100644 index 00000000..cf910f55 --- /dev/null +++ b/usegalaxy.org/seurat.yml.lock @@ -0,0 +1,83 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Seurat +tools: +- name: seurat_create_seurat_object + owner: ebi-gxa + revisions: + - f8865ae30723 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_export_cellbrowser + owner: ebi-gxa + revisions: + - 36221da750e8 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_filter_cells + owner: ebi-gxa + revisions: + - cd9f564bd63f + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_clusters + owner: ebi-gxa + revisions: + - d541e9e62beb + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_markers + owner: ebi-gxa + revisions: + - 07fc9f4841b3 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_neighbours + owner: ebi-gxa + revisions: + - ba897c57bdd9 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_find_variable_genes + owner: ebi-gxa + revisions: + - 948fc0276b4f + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_normalise_data + owner: ebi-gxa + revisions: + - 3f49bc9c9213 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_dim_plot + owner: ebi-gxa + revisions: + - 64174ac50d78 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_read10x + owner: ebi-gxa + revisions: + - f5db0e853f57 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_pca + owner: ebi-gxa + revisions: + - 8ded486b0014 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_run_tsne + owner: ebi-gxa + revisions: + - 0db997e4a81d + tool_panel_section_id: seurat + tool_panel_section_label: Seurat +- name: seurat_scale_data + owner: ebi-gxa + revisions: + - 5e9ba303f9e1 + tool_panel_section_id: seurat + tool_panel_section_label: Seurat diff --git a/usegalaxy.org/single_cell.yml b/usegalaxy.org/single_cell.yml index aa9cc326..a8a11fed 100644 --- a/usegalaxy.org/single_cell.yml +++ b/usegalaxy.org/single_cell.yml @@ -124,3 +124,13 @@ tools: owner: iuc - name: velocyto_cli owner: iuc +- name: gsc_scran_normalize + owner: artbio +- name: snapatac2_clustering + owner: iuc +- name: snapatac2_peaks_and_motif + owner: iuc +- name: snapatac2_plotting + owner: iuc +- name: snapatac2_preprocessing + owner: iuc diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock index 2dbb7415..7e805143 100644 --- a/usegalaxy.org/single_cell.yml.lock +++ b/usegalaxy.org/single_cell.yml.lock @@ -536,3 +536,33 @@ tools: - 90e95e9ee190 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell +- name: gsc_scran_normalize + owner: artbio + revisions: + - 6864acb21714 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_clustering + owner: iuc + revisions: + - 8f8bef61fd0b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_peaks_and_motif + owner: iuc + revisions: + - 588c811fdd48 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_plotting + owner: iuc + revisions: + - fecf9664c885 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: snapatac2_preprocessing + owner: iuc + revisions: + - cec3e76eaf05 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell diff --git a/usegalaxy.org/spatial.yml b/usegalaxy.org/spatial.yml new file mode 100644 index 00000000..85d64f88 --- /dev/null +++ b/usegalaxy.org/spatial.yml @@ -0,0 +1,14 @@ +tool_panel_section_label: Spatial +tools: +- name: quantification + owner: perssond +- name: cell_intensity_processing + owner: goeckslab +- name: s3segmenter + owner: perssond +- name: slice_image + owner: imgteam +- name: squidpy + owner: goeckslab +- name: vitessce_spatial + owner: goeckslab diff --git a/usegalaxy.org/spatial.yml.lock b/usegalaxy.org/spatial.yml.lock new file mode 100644 index 00000000..415c67d3 --- /dev/null +++ b/usegalaxy.org/spatial.yml.lock @@ -0,0 +1,41 @@ +install_repository_dependencies: true +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Spatial +tools: +- name: quantification + owner: perssond + revisions: + - 3a916c4e9f5f + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: cell_intensity_processing + owner: goeckslab + revisions: + - 5d541df02496 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: s3segmenter + owner: perssond + revisions: + - 96d0d969ebc9 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: slice_image + owner: imgteam + revisions: + - a72590196440 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: squidpy + owner: goeckslab + revisions: + - d30ef0613122 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial +- name: vitessce_spatial + owner: goeckslab + revisions: + - 7cc457aa78b1 + tool_panel_section_id: spatial + tool_panel_section_label: Spatial