add compute p-val

Delphine-L · Dec 1, 2023 · bc00f92 · bc00f92
1 parent d78dbfc
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diff --git 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
@@ -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
@@ -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 @@
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             "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,
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@@ -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",
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                 "tool_shed": "toolshed.g2.bx.psu.edu"
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-            "tool_version": "1.1.2+galaxy0",
+            "tool_version": "1.1.2+galaxy1",
             "type": "tool",
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@@ -524,7 +524,7 @@
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@@ -567,15 +567,15 @@
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+            "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",
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                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
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-            "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
@@ -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
@@ -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"
@@ -456,22 +483,22 @@
                     }
                 },
                 "tags": "",
-                "uuid": "8892c067-c08f-4ed9-83c0-9e03ccab02da"
+                "uuid": "e00a82b6-374c-436b-a5fa-c4b316ecdee8"
             },
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             "type": "subworkflow",
             "uuid": "e5607959-5b5e-4898-92ab-078c7cafb327",
             "when": null,
             "workflow_outputs": []
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-        "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"
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             "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"
             },
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-            "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"
-                },
-                {
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-                    "output_name": "pdf2d",
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                 }
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         }
     },
     "tags": [],
-    "uuid": "399b7c15-e670-442c-8bfc-2e5b97644115",
-    "version": 5
+    "uuid": "1936816b-958a-4140-b839-58be4cdae1a5",
+    "version": 1
 }