diff --git a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/workflows/Galaxy-Workflow-Workflow_constructed_from_history__Tool_based_FPE_ (1).ga b/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/workflows/Galaxy-Workflow-Workflow_constructed_from_history__Tool_based_FPE_ (1).ga deleted file mode 100644 index 61488823f0dfeb..00000000000000 --- a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/workflows/Galaxy-Workflow-Workflow_constructed_from_history__Tool_based_FPE_ (1).ga +++ /dev/null @@ -1,527 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "comments": [], - "format-version": "0.1", - "name": "Workflow constructed from history 'Tool based FPE'", - "steps": { - "0": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2", - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [], - "label": null, - "name": "EBI SCXA Data Retrieval", - "outputs": [ - { - "name": "matrix_mtx", - "type": "txt" - }, - { - "name": "genes_tsv", - "type": "tsv" - }, - { - "name": "barcode_tsv", - "type": "tsv" - }, - { - "name": "design_tsv", - "type": "tsv" - } - ], - "position": { - "left": 10, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2", - "tool_shed_repository": { - "changeset_revision": "72b6e1747e37", - "name": "retrieve_scxa", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"data\", \"accession\": \"E-MTAB-6945\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"matrix_type\": \"raw\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "v0.0.2+galaxy2", - "type": "tool", - "uuid": "08db272c-657f-4c37-a972-ad76319fb5f9", - "when": null, - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0", - "errors": null, - "id": 1, - "input_connections": { - "input|barcodes": { - "id": 0, - "output_name": "barcode_tsv" - }, - "input|genes": { - "id": 0, - "output_name": "genes_tsv" - }, - "input|matrix": { - "id": 0, - "output_name": "matrix_mtx" - }, - "metadata": { - "id": 0, - "output_name": "design_tsv" - } - }, - "inputs": [], - "label": null, - "name": "Seurat Read10x", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 230, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "f5db0e853f57", - "name": "seurat_read10x", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"mtx\", \"__current_case__\": 1, \"matrix\": null, \"genes\": null, \"barcodes\": null}, \"metadata\": null, \"min_cells\": \"5\", \"min_features\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "d01793f5-e8b6-4478-b11e-5fdaa02703b8", - "when": null, - "workflow_outputs": [] - }, - "2": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0", - "errors": null, - "id": 2, - "input_connections": { - "input|rds_seurat_file": { - "id": 1, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Plot", - "outputs": [ - { - "name": "plot_out_png", - "type": "png" - } - ], - "position": { - "left": 450, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "95d79f1134f0", - "name": "seurat_plot", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"bg\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dpi\": \"300\", \"enable_output_rds_file\": false, \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"limitsize\": true, \"plot_format\": \"png\", \"plot_type\": {\"plot_type_selector\": \"VlnPlot\", \"__current_case__\": 4, \"features\": \"nCount_RNA\", \"cols\": null, \"pt_size\": null, \"idents\": null, \"sort\": false, \"assay\": null, \"group_by\": null, \"split_by\": null, \"adjust\": \"1\", \"same_y_lims\": false, \"log\": true, \"ncol\": null, \"slot\": \"data\", \"split_plot\": false, \"stack\": false, \"fill_by\": \"feature\", \"flip\": false}, \"units\": \"cm\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "12226908-d4f0-44b7-a765-e73b917a3b12", - "when": null, - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0", - "errors": null, - "id": 3, - "input_connections": { - "input|rds_seurat_file": { - "id": 1, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat FilterCells", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 450, - "top": 130 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "cd9f564bd63f", - "name": "seurat_filter_cells", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"cells\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"subsets\": [{\"__index__\": 0, \"name\": \"nCount_RNA\", \"min\": \"500.0\", \"max\": \"10000.0\"}, {\"__index__\": 1, \"name\": \"nFeature_RNA\", \"min\": \"500.0\", \"max\": \"1000000000.0\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "3c3b2c00-d55f-4b9e-a723-6b393d59a72f", - "when": null, - "workflow_outputs": [] - }, - "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0", - "errors": null, - "id": 4, - "input_connections": { - "input|rds_seurat_file": { - "id": 3, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat NormaliseData", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 670, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "3f49bc9c9213", - "name": "seurat_normalise_data", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"assay\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"norm\": \"LogNormalize\", \"scale\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "7cae423b-0228-42d9-a987-9418f04e620f", - "when": null, - "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0", - "errors": null, - "id": 5, - "input_connections": { - "input|rds_seurat_file": { - "id": 4, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat FindVariableGenes", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - }, - { - "name": "output_tab", - "type": "tabular" - } - ], - "position": { - "left": 890, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "948fc0276b4f", - "name": "seurat_find_variable_genes", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"disp\": null, \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"mean\": null, \"nfeatures\": null, \"selection_method\": \"vst\", \"xhigh\": null, \"xlow\": null, \"yhigh\": null, \"ylow\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "b9bddcea-105c-47e3-9f83-f513c9e3dc68", - "when": null, - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0", - "errors": null, - "id": 6, - "input_connections": { - "genes_use": { - "id": 5, - "output_name": "output_tab" - }, - "input|rds_seurat_file": { - "id": 5, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat ScaleData", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 1110, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "5e9ba303f9e1", - "name": "seurat_scale_data", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"block_size\": null, \"check_for_norm\": false, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"do_not_center\": false, \"do_not_scale\": false, \"format\": \"rds_seurat\", \"genes_use\": null, \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"min_cells_to_block\": null, \"model\": \"linear\", \"scale_max\": null, \"use_umi\": false, \"vars\": \"nCount_RNA\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "7e9ddc40-5636-4e38-ab22-4eda2cc484d6", - "when": null, - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0", - "errors": null, - "id": 7, - "input_connections": { - "input|rds_seurat_file": { - "id": 6, - "output_name": "rds_seurat_file" - }, - "pc_genes": { - "id": 5, - "output_name": "output_tab" - } - }, - "inputs": [], - "label": null, - "name": "Seurat RunPCA", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - }, - { - "name": "output_embed", - "type": "csv" - }, - { - "name": "output_load", - "type": "csv" - }, - { - "name": "output_sdev", - "type": "csv" - } - ], - "position": { - "left": 1330, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "8ded486b0014", - "name": "seurat_run_pca", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"pc_cells\": null, \"pc_genes\": null, \"pcs_compute\": null, \"reverse_pca\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "e98a8c81-1a01-490f-b887-b65eb831abeb", - "when": null, - "workflow_outputs": [] - }, - "8": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0", - "errors": null, - "id": 8, - "input_connections": { - "input|rds_seurat_file": { - "id": 7, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat FindNeighbours", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 1550, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "ba897c57bdd9", - "name": "seurat_find_neighbours", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"annoy_metric\": \"euclidean\", \"assay\": \"RNA\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"compute_snn\": false, \"dims\": \"1,2,3,4,5,6,7,8,9,10,11,12,13,14,15\", \"distance_matrix\": false, \"do_plot\": false, \"features\": null, \"features_file\": null, \"force_recalc\": false, \"format\": \"rds_seurat\", \"graph_name\": null, \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"k_param\": null, \"nn_eps\": null, \"nn_method\": \"rann\", \"prune_snn\": null, \"reduction\": \"pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "8c604e31-5f4b-437e-b8da-3c4c5d494911", - "when": null, - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0", - "errors": null, - "id": 9, - "input_connections": { - "input|rds_seurat_file": { - "id": 8, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat FindClusters", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - }, - { - "name": "output_tab", - "type": "csv" - } - ], - "position": { - "left": 1770, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "d541e9e62beb", - "name": "seurat_find_clusters", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"resolution\": \"0.5\", \"algorithm\": \"1\", \"modularity_fxn\": \"1\", \"method\": \"matrix\", \"graph_name\": \"RNA_nn\", \"nrandom_starts\": null, \"group_singletons\": false, \"random_seed\": null}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "6001ccc3-dc17-455f-b733-54caead5f182", - "when": null, - "workflow_outputs": [] - }, - "10": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0", - "errors": null, - "id": 10, - "input_connections": { - "input|rds_seurat_file": { - "id": 9, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Seurat UMAP", - "outputs": [ - { - "name": "rds_seurat_file", - "type": "rdata" - } - ], - "position": { - "left": 1990, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "b9424c715a0d", - "name": "seurat_run_umap", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"graph\": null, \"nn_name\": null, \"slot\": \"data\", \"umap_method\": \"uwot\", \"reduction_model\": null, \"return_model\": false, \"metric\": \"cosine\", \"n_epochs\": null, \"learning_rate\": \"1\", \"min_dist\": \"0\", \"spread\": \"1\", \"repulsion_strength\": \"1\", \"negative_sample_rate\": \"5\", \"a\": null, \"b\": null, \"uwot_sgd\": false, \"angular_rp_forest\": false, \"verbose\": true}, \"assay\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dims\": \"1:15\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"local_connectivity\": \"1\", \"n_components\": \"2\", \"n_neighbors\": \"30\", \"reduction\": \"pca\", \"reduction_key\": \"UMAP\", \"reduction_name\": \"umap\", \"seed_use\": \"42\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "e3c8a7f0-b5e4-4d7d-adb1-361a4174fd52", - "when": null, - "workflow_outputs": [] - }, - "11": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0", - "errors": null, - "id": 11, - "input_connections": { - "input|rds_seurat_file": { - "id": 10, - "output_name": "rds_seurat_file" - } - }, - "inputs": [], - "label": null, - "name": "Plot", - "outputs": [ - { - "name": "plot_out_png", - "type": "png" - } - ], - "position": { - "left": 2210, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0", - "tool_shed_repository": { - "changeset_revision": "95d79f1134f0", - "name": "seurat_plot", - "owner": "ebi-gxa", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"bg\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dpi\": \"300\", \"enable_output_rds_file\": false, \"input\": {\"format\": \"rds_seurat\", \"__current_case__\": 2, \"rds_seurat_file\": null}, \"limitsize\": true, \"plot_format\": \"png\", \"plot_type\": {\"plot_type_selector\": \"DimPlot\", \"__current_case__\": 0, \"dims\": \"1,2\", \"cells\": null, \"cols\": null, \"pt_size\": null, \"reduction\": null, \"group_by\": \"RNA_nn_res.0.5\", \"split_by\": null, \"shape_by\": null, \"order\": null, \"shuffle\": false, \"seed\": \"1\", \"label\": false, \"label_size\": \"4\", \"label_color\": \"black\", \"label_box\": false, \"repel\": false, \"cells_highlight\": null, \"cols_highlight\": \"#DE2D26\", \"sizes_highlight\": \"1\", \"na_value\": \"grey50\", \"ncol\": null}, \"units\": \"cm\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0.4+galaxy0", - "type": "tool", - "uuid": "22647cf6-4feb-45c9-bd04-56328976f48b", - "when": null, - "workflow_outputs": [] - } - }, - "tags": [], - "uuid": "d43ce265-c97e-4057-a5b6-7aa8b3436d4d", - "version": 0 -} \ No newline at end of file