workflow tests

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Cell-Data-Set-(CDS)-conversion-test.yml

@@ -0,0 +1,15 @@
+- doc: Test outline for AnnData-to-Cell-Data-Set-(CDS)-conversion
+  job:
+    AnnData:
+      class: File
+      path: test-data/AnnData.h5ad
+      filetype: h5ad
+  outputs:
+    'Inspect AnnData: var':
+      path: 'test-data/Inspect AnnData: var.tabular'
+    CDS Monocle file:
+      path: test-data/CDS Monocle file.rdata
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Cell-Data-Set-(CDS)-conversion.ga

@@ -0,0 +1 @@
+{"a_galaxy_workflow": "true", "annotation": "AnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols. ", "creator": [{"class": "Person", "identifier": "0009-0001-2017-8805", "name": "Julia Jakiela"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "AnnData to Cell Data Set (CDS) conversion", "steps": {"0": {"annotation": "Input file in AnnData format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "Input file in AnnData format", "name": "AnnData"}], "label": "AnnData", "name": "Input dataset", "outputs": [], "position": {"left": 0, "top": 0}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "803b5429-24a8-4ba8-b9f0-d9012a23d190", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "errors": null, "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "label": null, "name": "Inspect AnnData", "outputs": [{"name": "obs", "type": "tabular"}], "position": {"left": 256.73787564688695, "top": 79.01355786263034}, "post_job_actions": {"RenameDatasetActionobs": {"action_arguments": {"newname": "Cell barcodes"}, "action_type": "RenameDatasetAction", "output_name": "obs"}}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "tool_shed_repository": {"changeset_revision": "ee98d611afc6", "name": "anndata_inspect", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.7.5+galaxy1", "type": "tool", "uuid": "3dd0c427-0689-47b4-bfe4-1ad3127972d8", "when": null, "workflow_outputs": [{"label": "Inspect AnnData: obs", "output_name": "obs", "uuid": "7bdb825c-6a89-4a34-bbd9-a79c309c9750"}]}, "2": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "errors": null, "id": 2, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "label": null, "name": "Inspect AnnData", "outputs": [{"name": "var", "type": "tabular"}], "position": {"left": 298.0404350277319, "top": 221.00360766192858}, "post_job_actions": {"RenameDatasetActionvar": {"action_arguments": {"newname": "Genes"}, "action_type": "RenameDatasetAction", "output_name": "var"}}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "tool_shed_repository": {"changeset_revision": "ee98d611afc6", "name": "anndata_inspect", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.7.5+galaxy1", "type": "tool", "uuid": "dd941b59-7d88-4f2a-8241-9ce658bab555", "when": null, "workflow_outputs": [{"label": "Inspect AnnData: var", "output_name": "var", "uuid": "79a2e3e5-4bd6-42de-864c-a5dc2412cb86"}]}, "3": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "errors": null, "id": 3, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "label": null, "name": "Inspect AnnData", "outputs": [{"name": "X", "type": "tabular"}], "position": {"left": 362.5640208496929, "top": 368.5465046492902}, "post_job_actions": {"RenameDatasetActionX": {"action_arguments": {"newname": "Expression matrix"}, "action_type": "RenameDatasetAction", "output_name": "X"}}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "tool_shed_repository": {"changeset_revision": "ee98d611afc6", "name": "anndata_inspect", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.7.5+galaxy1", "type": "tool", "uuid": "535c49c0-591e-47b6-8816-20ee58cd7e37", "when": null, "workflow_outputs": [{"label": "Inspect AnnData: X", "output_name": "X", "uuid": "7a254954-7e32-4e8a-bd4c-a79abf9db8d8"}]}, "4": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1", "errors": null, "id": 4, "input_connections": {"in_file": {"id": 3, "output_name": "X"}}, "inputs": [], "label": null, "name": "Transpose", "outputs": [{"name": "out_file", "type": "input"}], "position": {"left": 599.440446949216, "top": 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null, "name": "Monocle3 create", "outputs": [{"name": "output_rds", "type": "rdata"}], "position": {"left": 848.1105796111376, "top": 495.7890097555672}, "post_job_actions": {"RenameDatasetActionoutput_rds": {"action_arguments": {"newname": "CDS Monocle file"}, "action_type": "RenameDatasetAction", "output_name": "output_rds"}}, "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2", "tool_shed_repository": {"changeset_revision": "ada68a9d0aec", "name": "monocle3_create", "owner": "ebi-gxa", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"cell_metadata\": {\"__class__\": \"ConnectedValue\"}, \"cell_metadata_format\": \"tsv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"expression_matrix\": {\"__class__\": \"ConnectedValue\"}, \"expression_matrix_format\": \"tsv\", \"gene_annotation\": {\"__class__\": \"ConnectedValue\"}, \"gene_annotation_format\": \"tsv\", \"introspective\": true, \"output_object_format\": \"cds3\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.4+galaxy2", "type": "tool", "uuid": "17a4bbe9-5a3c-4c54-b581-c24588ccf397", "when": null, "workflow_outputs": [{"label": "CDS Monocle file", "output_name": "output_rds", "uuid": "6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c"}]}}, "tags": [], "uuid": "d0ce033d-5669-475c-879b-ce5391b029aa", "version": 7}

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Seurat-conversion-test.yml

@@ -0,0 +1,13 @@
+- doc: Test outline for AnnData-to-Seurat-conversion
+  job:
+    AnnData:
+      class: File
+      path: test-data/AnnData.h5ad
+      filetype: h5ad
+  outputs:
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'
+    Converted Seurat object:
+      path: test-data/Converted Seurat object.rdata
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Seurat-conversion.ga

@@ -0,0 +1 @@
+{"a_galaxy_workflow": "true", "annotation": "AnnData to Seurat format conversion (manually using Galaxy buttons)", "creator": [{"class": "Person", "identifier": "0009-0001-2017-8805", "name": "Julia Jakiela"}, {"class": "Person", "identifier": "0009-0008-9422-6380", "name": "Morgan Howells"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "AnnData to Seurat conversion", "steps": {"0": {"annotation": "Input file in AnnData format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "Input file in AnnData format", "name": "AnnData"}], "label": "AnnData", "name": "Input dataset", "outputs": [], "position": {"left": 0, "top": 0}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f783e6c3-808c-4dd2-84dd-6130c8230970", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0", "errors": null, "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "label": null, "name": "Inspect AnnData", "outputs": [{"name": "obs", "type": "tabular"}], "position": {"left": 242.47774426074216, "top": 60.81245422363281}, "post_job_actions": {"RenameDatasetActionobs": {"action_arguments": {"newname": "Observations"}, "action_type": "RenameDatasetAction", "output_name": "obs"}}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0", "tool_shed_repository": {"changeset_revision": "6f0d0c784f09", "name": "anndata_inspect", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, 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"owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.10.3+galaxy0", "type": "tool", "uuid": "2d2961d5-fe61-4c57-af14-cad6f77e8ebc", "when": null, "workflow_outputs": [{"label": "Inspect AnnData: X", "output_name": "X", "uuid": "ea025a8a-6f3a-4e38-a3af-db406886c7de"}]}, "3": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1", "errors": null, "id": 3, "input_connections": {"in_file": {"id": 2, "output_name": "X"}}, "inputs": [], "label": null, "name": "Transpose", "outputs": [{"name": "out_file", "type": "input"}], "position": {"left": 524.1027526855469, "top": 414.38751220703125}, "post_job_actions": {}, "tool_id": 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{"name": "genes_out", "type": "tsv"}, {"name": "matrix_out", "type": "mtx"}], "position": {"left": 776.1026916503906, "top": 497.0278162336424}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2", "tool_shed_repository": {"changeset_revision": "a9caad671439", "name": "dropletutils", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"operation\": {\"use\": \"filter\", \"__current_case__\": 0, \"method\": {\"use\": \"defaultdrops\", \"__current_case__\": 0, \"expected\": \"338\", \"upperquant\": \"1.0\", \"lowerprop\": \"0.0\"}, \"outformat\": \"directory\"}, \"seed\": \"100\", \"tenx_format\": {\"use\": \"tsv\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.10.0+galaxy2", "type": "tool", "uuid": "f894f102-5f72-4323-a6c0-d389813b027a", "when": null, "workflow_outputs": []}, "5": {"annotation": "", 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topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion-test.yml

@@ -0,0 +1,14 @@
+- doc: Test outline for AnnData-to-SingleCellExperiment-(SCE)-conversion
+  job:
+    AnnData:
+      class: File
+      path: test-data/AnnData.h5ad
+      filetype: h5ad
+    Cell ID column: index
+  outputs:
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'
+    Converted SCE object:
+      path: test-data/Converted SCE object.rdata