From d4696d7e610021ffa2df4012b7aeda3b8a62872c Mon Sep 17 00:00:00 2001 From: Anil Thanki Date: Fri, 15 Nov 2024 16:00:17 +0000 Subject: [PATCH] Update Galaxy-Workflow-Persist-Seq-cell_cycle.ga to add filter tools (#13) * Update Galaxy-Workflow-Persist-Seq-cell_cycle.ga --------- Co-authored-by: Pablo Moreno --- .../Galaxy-Workflow-Persist-Seq-cell_cycle.ga | 549 ++++++++++++------ 1 file changed, 357 insertions(+), 192 deletions(-) diff --git a/SC-workflow/Persist-Seq/Galaxy-Workflow-Persist-Seq-cell_cycle.ga b/SC-workflow/Persist-Seq/Galaxy-Workflow-Persist-Seq-cell_cycle.ga index 7d7ebbb..a209122 100644 --- a/SC-workflow/Persist-Seq/Galaxy-Workflow-Persist-Seq-cell_cycle.ga +++ b/SC-workflow/Persist-Seq/Galaxy-Workflow-Persist-Seq-cell_cycle.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "Persist-Seq v0.3.6, Scanpy 1.9.3 (cell cycle)", + "annotation": "Persist-Seq v0.4.0, Scanpy 1.9.3 (cell cycle)", "creator": [ { "class": "Person", @@ -11,10 +11,15 @@ "class": "Person", "identifier": "0000-0002-9856-1679", "name": "Pablo Moreno" + }, + { + "class": "Person", + "identifier": "0000-0002-8941-444X", + "name": "Anil Thanki" } ], "format-version": "0.1", - "name": "Persist-Seq v0.3.6", + "name": "Persist-Seq v0.4.0", "steps": { "0": { "annotation": "", @@ -39,7 +44,7 @@ "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "3b1924c6-ed1d-4b22-a25f-941887c89c23", + "uuid": "350786b1-8509-4b63-8ca2-3626706b96b5", "workflow_outputs": [] }, "1": { @@ -65,7 +70,7 @@ "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "2e6e8a4d-33fb-4d0d-883e-a624fad54b50", + "uuid": "50d3e02a-612f-4549-b6af-f2c530bf52ef", "workflow_outputs": [] }, "2": { @@ -91,7 +96,7 @@ "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "a5b40e6b-08b7-43a5-ad9e-cf2127651e6c", + "uuid": 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{ - "id": 33, + "id": 35, "output_name": "output_h5ad" } }, @@ -1880,7 +2058,7 @@ ], "position": { "left": 3470.90625, - "top": 0 + "top": 0.0 }, "post_job_actions": { "HideDatasetActionoutput_h5ad": { @@ -1906,17 +2084,17 @@ "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"true\", \"__current_case__\": 0, \"r_source\": {\"__class__\": \"ConnectedValue\"}}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"true\", \"__current_case__\": 0, \"xlayers\": [{\"__index__\": 0, \"x_source\": {\"__class__\": \"ConnectedValue\"}, \"dest\": \"filtered\"}, {\"__index__\": 1, \"x_source\": {\"__class__\": \"ConnectedValue\"}, \"dest\": \"normalised\"}]}, 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null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "6a4cbeab-af00-4ca8-bab3-f9ba06da580f", + "uuid": "275052d3-52ed-4561-9163-0a2a12d3b2e5", "workflow_outputs": [] }, - "40": { + "42": { "annotation": "", "content_id": "__MERGE_COLLECTION__", "errors": null, - "id": 40, + "id": 42, "input_connections": { "inputs_0|input": { - "id": 37, + "id": 39, "output_name": "output_h5ad" }, "inputs_1|input": { - "id": 36, + "id": 38, "output_name": "output" } }, @@ -1996,21 +2174,21 @@ "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "f3a9ab98-d806-47f1-827f-e5386d128063", + "uuid": "eddea676-55a2-423c-885e-beb42053845e", "workflow_outputs": [] }, - "41": { + "43": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "errors": null, - "id": 41, + "id": 43, "input_connections": { "copy_x|xlayers_0|x_source": { - "id": 24, + "id": 26, "output_name": "output_h5ad" }, "input_obj_file": { - "id": 38, + "id": 40, "output_name": "output_h5ad" } }, @@ -2051,21 +2229,21 @@ "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"true\", \"__current_case__\": 0, \"xlayers\": [{\"__index__\": 0, \"x_source\": {\"__class__\": \"ConnectedValue\"}, \"dest\": \"log_normalised_unscaled\"}]}, \"field_unique\": \"\", \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "d58ef447-0dd7-4dd0-bc1f-aa85a663215e", + "uuid": "527d7c0f-9e58-4e33-a5a6-20645c20226f", "workflow_outputs": [] }, - "42": { + "44": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "errors": null, - "id": 42, + "id": 44, "input_connections": { "copy_r|r_source": { - "id": 24, + "id": 26, "output_name": "output_h5ad" }, "input_obj_file": { - "id": 40, + "id": 42, "output_name": "output" } }, @@ -2104,21 +2282,21 @@ "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"true\", \"__current_case__\": 0, \"r_source\": {\"__class__\": \"ConnectedValue\"}}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "5b822bad-af30-4b99-a304-ff86e93618bd", + "uuid": "a17efa6d-62ee-4173-bcdf-24949d2de947", "workflow_outputs": [] }, - "43": { + "45": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "errors": null, - "id": 43, + "id": 45, "input_connections": { "copy_e|embedding_sources": { - "id": 34, + "id": 36, "output_name": "output" }, "input_obj_file": { - "id": 41, + "id": 43, "output_name": "output_h5ad" } }, @@ -2159,21 +2337,21 @@ "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"true\", \"__current_case__\": 0, \"embedding_keys\": [{\"__index__\": 0, \"contains\": \"tsne\"}], \"embedding_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"field_unique\": \"\", \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "dd187a1a-7873-488c-8547-658555129a36", + "uuid": "6af055dc-db53-47c7-b899-69baecbb9088", "workflow_outputs": [] }, - "44": { + "46": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.9.3+galaxy0", "errors": null, - "id": 44, + "id": 46, "input_connections": { "groupby_file": { "id": 20, "output_name": "output" }, "input_obj_file": { - "id": 42, + "id": 44, "output_name": "output_h5ad" } }, @@ -2223,27 +2401,27 @@ "tool_state": "{\"groupby\": \"INPUT_OBJ\", \"groupby_file\": {\"__class__\": \"ConnectedValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"100\", \"output_format\": \"anndata_h5ad\", \"output_markers\": \"true\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"key_added\": \"markers_GROUPBY\", \"method\": \"wilcoxon\", \"use_raw\": \"true\", \"rankby_abs\": \"false\", \"groups\": \"\", \"reference\": \"rest\", \"filter\": {\"default\": \"false\", \"__current_case__\": 1, \"min_in_group_fraction\": \"0.0\", \"max_out_group_fraction\": \"1.0\", \"min_fold_change\": \"2.0\"}, \"layer\": \"\", \"pts\": \"false\", \"tie_correct\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "fdfe2b36-a7c6-4d01-9db2-d6584be30bbb", + "uuid": "9b36e9e8-1929-4d72-924f-2c333ae3ec5b", "workflow_outputs": [ { "label": null, "output_name": "output_tsv", - "uuid": "bfba8baf-39fb-4a6c-bab1-1566a5cb4e71" + "uuid": "98e51399-7efa-4ea8-b9b2-a484cc52bdbd" } ] }, - "45": { + "47": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "errors": null, - "id": 45, + "id": 47, "input_connections": { "copy_e|embedding_sources": { - "id": 39, + "id": 41, "output_name": "output" }, "input_obj_file": { - "id": 43, + "id": 45, "output_name": "output_h5ad" } }, @@ -2284,17 +2462,17 @@ "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"true\", \"__current_case__\": 0, \"embedding_keys\": [{\"__index__\": 0, \"contains\": \"umap\"}], \"embedding_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"field_unique\": \"\", \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "77bc1385-2827-4558-b555-3f45979d4b7e", + "uuid": "ce36c7c7-eb57-4896-a3f7-bb0fb54e709c", "workflow_outputs": [] }, - "46": { + "48": { "annotation": "", "content_id": "__FILTER_FAILED_DATASETS__", "errors": null, - "id": 46, + "id": 48, "input_connections": { "input": { - "id": 44, + "id": 46, "output_name": "output_h5ad" } }, @@ -2327,42 +2505,29 @@ "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "85015e1b-9900-40e4-89ae-ee6d1c75935b", + "uuid": "7e3a0a0f-895a-416d-87f7-f6f3678d58c1", "workflow_outputs": [] }, - "47": { + "49": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0", "errors": null, - "id": 47, + "id": 49, "input_connections": { "copy_o|obs_sources": { - "id": 46, + "id": 48, "output_name": "output" }, "copy_u|uns_sources": { - "id": 46, + "id": 48, "output_name": "output" }, "input_obj_file": { - "id": 45, + "id": 47, "output_name": "output_h5ad" } }, - "inputs": [ - { - "description": "runtime parameter for tool AnnData Operations", - "name": "copy_o" - }, - { - "description": "runtime parameter for tool AnnData Operations", - "name": "copy_u" - }, - { - "description": "runtime parameter for tool AnnData Operations", - "name": "input_obj_file" - } - ], + "inputs": [], "label": "final_project_file", "name": "AnnData Operations", "outputs": [ @@ -2391,20 +2556,20 @@ "owner": "ebi-gxa", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"true\", \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"RuntimeValue\"}}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"true\", \"__current_case__\": 0, \"uns_keys\": [{\"__index__\": 0, \"contains\": \"marker\"}], \"uns_sources\": {\"__class__\": \"RuntimeValue\"}}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"field_unique\": \"gene_symbols\", \"gene_flags\": [], \"gene_symbols_field\": \"gene_symbols\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"true\", \"__current_case__\": 0, \"layer\": \"log_normalised_unscaled\", \"new_name_x\": \"log_normalised_scaled_zero_centered\"}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"add_cell_metadata\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"true\", \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"true\", \"__current_case__\": 0, \"uns_keys\": [{\"__index__\": 0, \"contains\": \"marker\"}], \"uns_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"field_unique\": \"gene_symbols\", \"gene_flags\": [], \"gene_symbols_field\": \"gene_symbols\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"split_on_obs\": {\"default\": \"false\", \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": \"true\", \"__current_case__\": 0, \"layer\": \"log_normalised_unscaled\", \"new_name_x\": \"log_normalised_scaled_zero_centered\"}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.9.3+galaxy0", "type": "tool", - "uuid": "91bd3f1a-b81e-4682-a0e2-e6f0a2dbb1d2", + "uuid": "26e439ba-8490-42c7-a087-09ad8e0e231f", "workflow_outputs": [ { "label": null, "output_name": "output_h5ad", - "uuid": "a9838d28-e7a4-432d-b8d5-30a34b5a51e6" + "uuid": "1c1cbd08-8999-4ec3-b936-8a5ddbbc972e" } ] } }, "tags": [], - "uuid": "4f5d0ffa-608b-4618-bc0b-40dacff3bbfc", - "version": 11 + "uuid": "8c6ebec5-9c60-4b78-b3a3-dd1007130744", + "version": 7 }