diff workflow/ppenrich_suite_wf.ga @ 0:c1403d18c189 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
author eschen42
date Mon, 07 Mar 2022 19:05:01 +0000
parents
children d728198f1ba5
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflow/ppenrich_suite_wf.ga	Mon Mar 07 19:05:01 2022 +0000
@@ -0,0 +1,653 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "phoshpoproteomic enrichment data pre-processing and ANOVA",
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "0000-0002-2882-0508",
+            "name": "Art Eschenlauer"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "ppenrich_suite_wf",
+    "steps": {
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+            "label": "Phospho (STY)Sites.txt",
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+                    "name": "pSTY_Motifs.tabular"
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+            "label": "pSTY_Motifs.tabular",
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+            "content_id": null,
+            "errors": null,
+            "id": 4,
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+                {
+                    "description": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
+                    "name": "PSP_Kinase_Substrate_Dataset.tabular"
+                }
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+            "label": "PSP_Kinase_Substrate_Dataset.tabular",
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+                    "name": "PSP_Regulatory_sites.tabular"
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+                    "uuid": "a1a4f827-1f1f-4175-ae51-c238f9e1f248"
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+            "label": "MaxQuant Phosphopeptide ANOVA group-median imputed",
+            "name": "MaxQuant Phosphopeptide ANOVA",
+            "outputs": [
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+                    "name": "imputed_data_file",
+                    "type": "tabular"
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+                    "label": "intensities_group-mean-imputed_report",
+                    "output_name": "report_file",
+                    "uuid": "dfe9b34e-1f3e-4971-8382-41178104e253"
+                }
+            ]
+        },
+        "9": {
+            "annotation": "Perform ANOVA. For imputing missing values, create random values.",
+            "content_id": "mqppep_anova",
+            "errors": null,
+            "id": 9,
+            "input_connections": {
+                "alpha_file": {
+                    "id": 6,
+                    "output_name": "output"
+                },
+                "input_file": {
+                    "id": 7,
+                    "output_name": "preproc_tab"
+                }
+            },
+            "inputs": [],
+            "label": "MaxQuant Phosphopeptide ANOVA randomly imputed",
+            "name": "MaxQuant Phosphopeptide ANOVA",
+            "outputs": [
+                {
+                    "name": "imputed_data_file",
+                    "type": "tabular"
+                },
+                {
+                    "name": "report_file",
+                    "type": "html"
+                }
+            ],
+            "position": {
+                "bottom": 1325.0999603271484,
+                "height": 254.93333435058594,
+                "left": 1452.949951171875,
+                "right": 1652.949951171875,
+                "top": 1070.1666259765625,
+                "width": 200,
+                "x": 1452.949951171875,
+                "y": 1070.1666259765625
+            },
+            "post_job_actions": {
+                "RenameDatasetActionimputed_data_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_randomly-imputed_QN_LT"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "imputed_data_file"
+                },
+                "RenameDatasetActionreport_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_randomly-imputed_report (download/unzip to view)"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "report_file"
+                }
+            },
+            "tool_id": "mqppep_anova",
+            "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"first_data_column\": \"Intensity\", \"imputation\": {\"imputation_method\": \"random\", \"__current_case__\": 3, \"meanPercentile\": \"1\", \"sdPercentile\": \"0.2\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"sample_grouping_regex\": \"(\\\\d+)\", \"sample_names_regex\": \"\\\\.(\\\\d+)[A-Z]$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "0.1.0+galaxy0",
+            "type": "tool",
+            "uuid": "9516971c-8532-4797-8bf9-4655ff104dbd",
+            "workflow_outputs": [
+                {
+                    "label": "intensities_randomly-imputed_QN_LT",
+                    "output_name": "imputed_data_file",
+                    "uuid": "8ceda029-d5fd-4d75-a2b3-ac582bb137c3"
+                },
+                {
+                    "label": "intensities_randomly-imputed_report",
+                    "output_name": "report_file",
+                    "uuid": "84bedf25-c15b-4cc7-97e0-92f746e89f9c"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "ppenrich"
+    ],
+    "uuid": "ac7bf2d1-89fe-4bf6-920a-d5508842d3f9",
+    "version": 7
+}
\ No newline at end of file