Merge pull request galaxyproject#312 from lldelisle/update_baredSC

Update bared sc WF
Delphine-L · Dec 5, 2023 · f16a254 · f16a254
2 parents 7ff1b3f + bc00f92
commit f16a254
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diff --git a/workflows/scRNAseq/baredsc/CHANGELOG.md b/workflows/scRNAseq/baredsc/CHANGELOG.md
@@ -1,5 +1,15 @@
 # Changelog
 
+## [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`
+
 ## [0.1] 2023-10-03
 
 First release.
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
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1",
+    "release": "0.2",
     "name": "baredSC_1d_logNorm",
     "steps": {
         "0": {
@@ -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"
@@ -318,7 +318,7 @@
                     },
                     "4": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
@@ -347,15 +347,15 @@
                                 "output_name": "list_output_tab"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6cbe2f30c2d7",
+                            "changeset_revision": "baabc30154cd",
                             "name": "split_file_to_collection",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"split_parms\": {\"select_ftype\": \"tabular\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"top\": \"0\", \"split_by\": {\"select_split_by\": \"row\", \"__current_case__\": 1, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"split_file\", \"select_allocate\": {\"allocate\": \"byrow\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0",
+                        "tool_version": "0.5.1",
                         "type": "tool",
                         "uuid": "b621baec-46f7-4dfe-b6fa-f8c44c2822f2",
                         "when": null,
@@ -402,7 +402,7 @@
                     }
                 },
                 "tags": "",
-                "uuid": "7b292353-e3cc-4fa9-8898-b4d3e3ea4901"
+                "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
@@ -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: