From bc00f92b48a7a7ef192cc2e2513462b5dfcc00c1 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 1 Dec 2023 17:11:30 +0100 Subject: [PATCH] add compute p-val --- workflows/scRNAseq/baredsc/CHANGELOG.md | 8 +- workflows/scRNAseq/baredsc/README.md | 1 + .../scRNAseq/baredsc/baredSC-1d-logNorm.ga | 20 ++-- .../baredsc/baredSC-2d-logNorm-tests.yml | 3 +- .../scRNAseq/baredsc/baredSC-2d-logNorm.ga | 95 ++++++++++++------- 5 files changed, 82 insertions(+), 45 deletions(-) diff --git a/workflows/scRNAseq/baredsc/CHANGELOG.md b/workflows/scRNAseq/baredsc/CHANGELOG.md index ab48a688e..8e48d665e 100644 --- a/workflows/scRNAseq/baredsc/CHANGELOG.md +++ b/workflows/scRNAseq/baredsc/CHANGELOG.md @@ -1,10 +1,14 @@ # Changelog -## [0.2] 2023-11-28 +## [0.2] 2023-12-01 + +### Add 'compute p-value' parameter in 2d + +### Semi-automatic update +- all baredsc tools were updated from `1.1.2+galaxy0` to `1.1.2+galaxy1` ### Automatic update - `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1` -- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1` ## [0.1] 2023-10-03 diff --git a/workflows/scRNAseq/baredsc/README.md b/workflows/scRNAseq/baredsc/README.md index 1331dfa85..bbd9591e8 100644 --- a/workflows/scRNAseq/baredsc/README.md +++ b/workflows/scRNAseq/baredsc/README.md @@ -29,6 +29,7 @@ For the 2D: - maximum value in logNorm for x-axis: The maximum value to explore in PDF in the x axis. This value should be large enough so the PDF is at 0 at this value. - maximum value in logNorm for y-axis: The maximum value to explore in PDF in the y axis. This value should be large enough so the PDF is at 0 at this value. - Maximum number of Gaussians to study: All models between models with 1 2D-Gaussians to models with this number of 2D-Gaussians will be combined. +- compute p-value: Whether you want to get a p-value. As a consequence, less samples than available will be used for plots as p-value computation requires to have independent samples. ## Processing diff --git a/workflows/scRNAseq/baredsc/baredSC-1d-logNorm.ga b/workflows/scRNAseq/baredsc/baredSC-1d-logNorm.ga index a72a9fff4..5e4eac61d 100644 --- a/workflows/scRNAseq/baredsc/baredSC-1d-logNorm.ga +++ b/workflows/scRNAseq/baredsc/baredSC-1d-logNorm.ga @@ -226,7 +226,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -402,7 +402,7 @@ } }, "tags": "", - "uuid": "d744d431-46b6-4663-908d-cfb63a367be6" + "uuid": "5b8cec6f-f1c0-4797-80b6-c07dba176b35" }, "tool_id": null, "type": "subworkflow", @@ -412,7 +412,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_1d/baredsc_1d/1.1.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_1d/baredsc_1d/1.1.2+galaxy1", "errors": null, "id": 5, "input_connections": { @@ -492,15 +492,15 @@ "output_name": "plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_1d/baredsc_1d/1.1.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_1d/baredsc_1d/1.1.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "4fff5a293013", + "changeset_revision": "0e70b2dfe4be", "name": "baredsc_1d", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"MCMC\": {\"xmin\": \"0.0\", \"xmax\": {\"__class__\": \"ConnectedValue\"}, \"nx\": \"100\", \"minScalex\": \"0.1\", \"scale\": {\"type\": \"Seurat\", \"__current_case__\": 0, \"targetSum\": \"10000.0\"}, \"seed\": \"1\", \"nnorm\": {\"__class__\": \"ConnectedValue\"}, \"nsampMCMC\": \"100000\", \"automaticRestart\": {\"set_minNeff\": \"yes\", \"__current_case__\": 0, \"minNeff\": \"200.0\"}}, \"advanced\": {\"osampx\": \"10\", \"osampxpdf\": \"5\", \"coviscale\": \"1.0\", \"nis\": \"1000\", \"burn\": {\"custom\": \"no\", \"__current_case__\": 0}}, \"filter\": {\"nb\": \"0\", \"__current_case__\": 0}, \"geneColName\": {\"__class__\": \"ConnectedValue\"}, \"input_counts\": {\"filetype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"plots\": {\"image_file_format\": \"png\", \"title\": \"\", \"removeFirstSamples\": \"-1\", \"nsampInPlot\": \"100000\", \"prettyBins\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2+galaxy0", + "tool_version": "1.1.2+galaxy1", "type": "tool", "uuid": "75379c38-7040-4651-b875-5ad7382de31d", "when": null, @@ -524,7 +524,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_1d/baredsc_combine_1d/1.1.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_1d/baredsc_combine_1d/1.1.2+galaxy1", "errors": null, "id": 6, "input_connections": { @@ -567,15 +567,15 @@ "top": 170.5 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_1d/baredsc_combine_1d/1.1.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_1d/baredsc_combine_1d/1.1.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "050cf43887d3", + "changeset_revision": "b13d3e4c48e1", "name": "baredsc_combine_1d", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"MCMC\": {\"outputs\": {\"__class__\": \"ConnectedValue\"}, \"xmin\": \"0.0\", \"xmax\": {\"__class__\": \"ConnectedValue\"}, \"nx\": \"100\", \"minScalex\": \"0.1\", \"scale\": {\"type\": \"Seurat\", \"__current_case__\": 0, \"targetSum\": \"10000.0\"}, \"seed\": \"1\"}, \"advanced\": {\"osampx\": \"10\", \"osampxpdf\": \"5\", \"coviscale\": \"1.0\", \"nis\": \"1000\"}, \"filter\": {\"nb\": \"0\", \"__current_case__\": 0}, \"geneColName\": {\"__class__\": \"ConnectedValue\"}, \"input_counts\": {\"filetype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"plots\": {\"image_file_format\": \"png\", \"title\": \"\", \"removeFirstSamples\": \"-1\", \"nsampInPlot\": \"100000\", \"prettyBins\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2+galaxy0", + "tool_version": "1.1.2+galaxy1", "type": "tool", "uuid": "752ba293-93e9-4769-85d0-ebc9c2c100b6", "when": null, diff --git a/workflows/scRNAseq/baredsc/baredSC-2d-logNorm-tests.yml b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm-tests.yml index c6a8b61fb..7f5a7bd9a 100644 --- a/workflows/scRNAseq/baredsc/baredSC-2d-logNorm-tests.yml +++ b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm-tests.yml @@ -9,6 +9,7 @@ maximum value in logNorm for x-axis: '2.5' maximum value in logNorm for y-axis: '2.5' Maximum number of Gaussians to study: '4' + compute p-value: 'true' outputs: baredsc_numpy: element_tests: @@ -138,7 +139,7 @@ has_text_matching: expression: "0.89[0-9]*" has_text: - text: "mean\tmedian\tlow\thigh" + text: "mean\tmedian\tlow\thigh\tpval\terror" individuals: asserts: has_size: diff --git a/workflows/scRNAseq/baredsc/baredSC-2d-logNorm.ga b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm.ga index 2ab5d3740..b10266058 100644 --- a/workflows/scRNAseq/baredsc/baredSC-2d-logNorm.ga +++ b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm.ga @@ -164,8 +164,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 382, - "top": 507 + "left": 320, + "top": 481 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}", @@ -176,8 +176,35 @@ "workflow_outputs": [] }, "6": { - "annotation": "", + "annotation": "Whether you want to get a p-value. As a consequence, less samples than available will be used for plots.", + "content_id": null, + "errors": null, "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "Whether you want to get a p-value. As a consequence, less samples than available will be used for plots.", + "name": "compute p-value" + } + ], + "label": "compute p-value", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 378, + "top": 578.5 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "4b7990a3-4fff-4c74-a9ee-0a8716e33866", + "when": null, + "workflow_outputs": [] + }, + "7": { + "annotation": "", + "id": 7, "input_connections": { "Maximum number in param output": { "id": 5, @@ -280,7 +307,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "ddf54b12c295", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -456,7 +483,7 @@ } }, "tags": "", - "uuid": "8892c067-c08f-4ed9-83c0-9e03ccab02da" + "uuid": "e00a82b6-374c-436b-a5fa-c4b316ecdee8" }, "tool_id": null, "type": "subworkflow", @@ -464,14 +491,14 @@ "when": null, "workflow_outputs": [] }, - "7": { + "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_2d/baredsc_2d/1.1.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_2d/baredsc_2d/1.1.2+galaxy1", "errors": null, - "id": 7, + "id": 8, "input_connections": { "MCMC|nnorm": { - "id": 6, + "id": 7, "output_name": "params_list" }, "MCMC|xmax": { @@ -563,19 +590,24 @@ "output_name": "plot" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_2d/baredsc_2d/1.1.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_2d/baredsc_2d/1.1.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "aa4a6f0916b4", + "changeset_revision": "344c2af50552", "name": "baredsc_2d", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"MCMC\": {\"xmin\": \"0.0\", \"xmax\": {\"__class__\": \"ConnectedValue\"}, \"nx\": \"25\", \"minScalex\": \"0.1\", \"ymin\": \"0.0\", \"ymax\": {\"__class__\": \"ConnectedValue\"}, \"ny\": \"25\", \"minScaley\": \"0.1\", \"scale\": {\"type\": \"Seurat\", \"__current_case__\": 0, \"targetSum\": \"10000.0\"}, \"seed\": \"1\", \"nnorm\": {\"__class__\": \"ConnectedValue\"}, \"nsampMCMC\": \"100000\", \"automaticRestart\": {\"set_minNeff\": \"yes\", \"__current_case__\": 0, \"minNeff\": \"200.0\"}}, \"advanced\": {\"osampx\": \"10\", \"osampxpdf\": \"4\", \"osampy\": \"10\", \"osampypdf\": \"4\", \"coviscale\": \"1.0\", \"nis\": \"1000\", \"burn\": {\"custom\": \"no\", \"__current_case__\": 0}, \"scalePrior\": \"0.3\"}, \"filter\": {\"nb\": \"0\", \"__current_case__\": 0}, \"geneXColName\": {\"__class__\": \"ConnectedValue\"}, \"geneYColName\": {\"__class__\": \"ConnectedValue\"}, \"input_counts\": {\"filetype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"plots\": {\"image_file_format\": \"png\", \"title\": \"\", \"removeFirstSamples\": \"-1\", \"nsampInPlot\": \"100000\", \"prettyBinsx\": \"-1\", \"prettyBinsy\": \"-1\", \"log1pColorScale\": false, \"splity\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2+galaxy0", + "tool_version": "1.1.2+galaxy1", "type": "tool", "uuid": "3fb4de69-9b40-4243-92fb-75553ff8ef09", "when": null, "workflow_outputs": [ + { + "label": "baredsc_qc_plots", + "output_name": "qc_plots", + "uuid": "005ef683-a231-4b3f-b8ef-125a1ffd2d91" + }, { "label": "baredsc_neff", "output_name": "neff", @@ -585,22 +617,17 @@ "label": "baredsc_numpy", "output_name": "output", "uuid": "2f026269-bd89-4c20-a0df-bd1387f549d4" - }, - { - "label": "baredsc_qc_plots", - "output_name": "qc_plots", - "uuid": "005ef683-a231-4b3f-b8ef-125a1ffd2d91" } ] }, - "8": { + "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_2d/baredsc_combine_2d/1.1.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_2d/baredsc_combine_2d/1.1.2+galaxy1", "errors": null, - "id": 8, + "id": 9, "input_connections": { "MCMC|outputs": { - "id": 7, + "id": 8, "output_name": "output" }, "MCMC|xmax": { @@ -622,6 +649,10 @@ "input_counts|input": { "id": 0, "output_name": "output" + }, + "advanced|getPVal": { + "id": 6, + "output_name": "output" } }, "inputs": [], @@ -650,19 +681,24 @@ "top": 199.5 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_2d/baredsc_combine_2d/1.1.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_2d/baredsc_combine_2d/1.1.2+galaxy1", "tool_shed_repository": { - "changeset_revision": "ae969fdb8442", + "changeset_revision": "1d77986f9ddc", "name": "baredsc_combine_2d", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"MCMC\": {\"outputs\": {\"__class__\": \"ConnectedValue\"}, \"xmin\": \"0.0\", \"xmax\": {\"__class__\": \"ConnectedValue\"}, \"nx\": \"25\", \"minScalex\": \"0.1\", \"ymin\": \"0.0\", \"ymax\": {\"__class__\": \"ConnectedValue\"}, \"ny\": \"25\", \"minScaley\": \"0.1\", \"scale\": {\"type\": \"Seurat\", \"__current_case__\": 0, \"targetSum\": \"10000.0\"}, \"seed\": \"1\"}, \"advanced\": {\"osampx\": \"10\", \"osampxpdf\": \"4\", \"osampy\": \"10\", \"osampypdf\": \"4\", \"coviscale\": \"1.0\", \"nis\": \"1000\", \"scalePrior\": \"0.3\"}, \"filter\": {\"nb\": \"0\", \"__current_case__\": 0}, \"geneXColName\": {\"__class__\": \"ConnectedValue\"}, \"geneYColName\": {\"__class__\": \"ConnectedValue\"}, \"input_counts\": {\"filetype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"plots\": {\"image_file_format\": \"png\", \"title\": \"\", \"removeFirstSamples\": \"-1\", \"nsampInPlot\": \"100000\", \"prettyBinsx\": \"-1\", \"prettyBinsy\": \"-1\", \"log1pColorScale\": false, \"splity\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2+galaxy0", + "tool_state": "{\"MCMC\": {\"outputs\": {\"__class__\": \"ConnectedValue\"}, \"xmin\": \"0.0\", \"xmax\": {\"__class__\": \"ConnectedValue\"}, \"nx\": \"25\", \"minScalex\": \"0.1\", \"ymin\": \"0.0\", \"ymax\": {\"__class__\": \"ConnectedValue\"}, \"ny\": \"25\", \"minScaley\": \"0.1\", \"scale\": {\"type\": \"Seurat\", \"__current_case__\": 0, \"targetSum\": \"10000.0\"}, \"seed\": \"1\"}, \"advanced\": {\"getPVal\": {\"__class__\": \"ConnectedValue\"}, \"osampx\": \"10\", \"osampxpdf\": \"4\", \"osampy\": \"10\", \"osampypdf\": \"4\", \"coviscale\": \"1.0\", \"nis\": \"1000\", \"scalePrior\": \"0.3\"}, \"filter\": {\"nb\": \"0\", \"__current_case__\": 0}, \"geneXColName\": {\"__class__\": \"ConnectedValue\"}, \"geneYColName\": {\"__class__\": \"ConnectedValue\"}, \"input_counts\": {\"filetype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"plots\": {\"image_file_format\": \"png\", \"title\": \"\", \"removeFirstSamples\": \"-1\", \"nsampInPlot\": \"100000\", \"prettyBinsx\": \"-1\", \"prettyBinsy\": \"-1\", \"log1pColorScale\": false, \"splity\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.2+galaxy1", "type": "tool", "uuid": "e4eebae4-0952-4d21-8bb6-d16d1b5397b3", "when": null, "workflow_outputs": [ + { + "label": "combined_pdf2d", + "output_name": "pdf2d", + "uuid": "0fff7566-a7d9-4dac-b77b-416e6a2f56ef" + }, { "label": "combined_pdf2d_flat", "output_name": "pdf2d_flat", @@ -677,16 +713,11 @@ "label": "combined_other_outputs", "output_name": "other_outputs", "uuid": "eca7f33c-3a1d-41d7-a56a-925167baf364" - }, - { - "label": "combined_pdf2d", - "output_name": "pdf2d", - "uuid": "0fff7566-a7d9-4dac-b77b-416e6a2f56ef" } ] } }, "tags": [], - "uuid": "399b7c15-e670-442c-8bfc-2e5b97644115", - "version": 5 + "uuid": "1936816b-958a-4140-b839-58be4cdae1a5", + "version": 1 } \ No newline at end of file