diff workflow/ppenrich_suite_wf.ga @ 13:b41a077af3aa draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
author eschen42
date Tue, 22 Mar 2022 20:47:40 +0000
parents
children 6679616d0c18
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflow/ppenrich_suite_wf.ga	Tue Mar 22 20:47:40 2022 +0000
@@ -0,0 +1,652 @@
+{
+    "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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+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "The Phospho (STY)Sites.txt file produced by MaxQuant (found in the txt folder).",
+                    "name": "Phospho (STY)Sites.txt"
+                }
+            ],
+            "label": "Phospho (STY)Sites.txt",
+            "name": "Input dataset",
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+            "inputs": [
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+                    "name": "SwissProt_Human_Canonical_Isoform.fasta"
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+            ],
+            "label": "SwissProt_Human_Canonical_Isoform.fasta",
+            "name": "Input dataset",
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+            "uuid": "5da7317c-4def-48f3-8eac-af95bd18b290",
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+        },
+        "2": {
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+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Derived from https://networkin.info/download/networkin_human_predictions_3.1.tsv.xz (which is free for non-commercial use - for required citation, see https://networkin.info/)",
+                    "name": "NetworKIN_cutoffscore2.0.tabular"
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+            ],
+            "label": "NetworKIN_cutoffscore2.0.tabular",
+            "name": "Input dataset",
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+        "3": {
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+            "content_id": null,
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+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
+                    "name": "pSTY_Motifs.tabular"
+                }
+            ],
+            "label": "pSTY_Motifs.tabular",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
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+            "uuid": "86ebaaf2-b050-4eca-a88b-23a4c1af39f5",
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+        "4": {
+            "annotation": "Derived from Kinase_Substrate_Dataset.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
+            "content_id": null,
+            "errors": null,
+            "id": 4,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "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"
+                }
+            ],
+            "label": "PSP_Kinase_Substrate_Dataset.tabular",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
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+            "annotation": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
+            "content_id": null,
+            "errors": null,
+            "id": 5,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Derived from Regulatory_sites.gz found at https://www.phosphosite.org/staticDownloads (free for non-commercial use  - see that link for citation.)",
+                    "name": "PSP_Regulatory_sites.tabular"
+                }
+            ],
+            "label": "PSP_Regulatory_sites.tabular",
+            "name": "Input dataset",
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+            "uuid": "5ab49d93-11e4-4e91-b30b-92269b319879",
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+        "6": {
+            "annotation": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
+            "content_id": null,
+            "errors": null,
+            "id": 6,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "List of alpha cutoff values for significance testing; text file having no header and a single line for each cutoff value.",
+                    "name": "alpha_levels.tabular"
+                }
+            ],
+            "label": "alpha_levels.tabular",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
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+            "uuid": "481c627c-a4ce-45d7-b659-4f54692aafc7",
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+                    "output_name": "output"
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+            "inputs": [],
+            "label": null,
+            "name": "MaxQuant Phosphopeptide Preprocessing",
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+                    "name": "phosphoPepIntensities",
+                    "type": "tabular"
+                },
+                {
+                    "name": "enrichGraph",
+                    "type": "pdf"
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+                {
+                    "name": "locProbCutoffGraph",
+                    "type": "pdf"
+                },
+                {
+                    "name": "enrichGraph_svg",
+                    "type": "svg"
+                },
+                {
+                    "name": "locProbCutoffGraph_svg",
+                    "type": "svg"
+                },
+                {
+                    "name": "filteredData_tabular",
+                    "type": "tabular"
+                },
+                {
+                    "name": "quantData_tabular",
+                    "type": "tabular"
+                },
+                {
+                    "name": "mapped_phophopeptides",
+                    "type": "tabular"
+                },
+                {
+                    "name": "melted_phophopeptide_map",
+                    "type": "tabular"
+                },
+                {
+                    "name": "mqppep_output_sqlite",
+                    "type": "sqlite"
+                },
+                {
+                    "name": "preproc_tab",
+                    "type": "tabular"
+                },
+                {
+                    "name": "preproc_csv",
+                    "type": "csv"
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+                {
+                    "name": "preproc_sqlite",
+                    "type": "sqlite"
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+                    "output_name": "enrichGraph_svg"
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+                    "action_type": "RenameDatasetAction",
+                    "output_name": "filteredData_tabular"
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+                    "action_arguments": {
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+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "locProbCutoffGraph"
+                },
+                "RenameDatasetActionlocProbCutoffGraph_svg": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.locProbCutoffGraph_svg"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "locProbCutoffGraph_svg"
+                },
+                "RenameDatasetActionmapped_phophopeptides": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.ppep_map"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "mapped_phophopeptides"
+                },
+                "RenameDatasetActionmelted_phophopeptide_map": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.melted"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "melted_phophopeptide_map"
+                },
+                "RenameDatasetActionmqppep_output_sqlite": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.ppep_mapping_sqlite"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "mqppep_output_sqlite"
+                },
+                "RenameDatasetActionphosphoPepIntensities": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.ppep_intensities"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "phosphoPepIntensities"
+                },
+                "RenameDatasetActionpreproc_csv": {
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+                        "newname": "#{phosphoSites}.preproc_csv"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "preproc_csv"
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+                "RenameDatasetActionpreproc_sqlite": {
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+                        "newname": "#{phosphoSites}.preproc_sqlite"
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+                    "action_type": "RenameDatasetAction",
+                    "output_name": "preproc_sqlite"
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+                "RenameDatasetActionpreproc_tab": {
+                    "action_arguments": {
+                        "newname": "#{phosphoSites}.preproc_tab"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "preproc_tab"
+                },
+                "RenameDatasetActionquantData_tabular": {
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+                        "newname": "#{phosphoSites}.quantData"
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+                    "action_type": "RenameDatasetAction",
+                    "output_name": "quantData_tabular"
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+            "tool_version": null,
+            "type": "tool",
+            "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85",
+            "workflow_outputs": [
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+                    "label": "preproc_csv",
+                    "output_name": "preproc_csv",
+                    "uuid": "8cba5367-b25c-40e0-a324-552225b1aa1d"
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+                    "output_name": "locProbCutoffGraph",
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+                    "uuid": "878dc817-26a3-4061-9dd4-56e737b3c4f7"
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+                {
+                    "label": "enrichGraph_svg",
+                    "output_name": "enrichGraph_svg",
+                    "uuid": "4492366c-945e-492f-8381-1c97c4da2264"
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+                {
+                    "label": "locProbCutoffGraph_svg",
+                    "output_name": "locProbCutoffGraph_svg",
+                    "uuid": "06faf93c-5f04-4cb3-9e41-58e465f6180e"
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+                {
+                    "label": "filteredData",
+                    "output_name": "filteredData_tabular",
+                    "uuid": "76e2e268-f728-45f0-9973-793fbde0dd0a"
+                },
+                {
+                    "label": "ppep_map",
+                    "output_name": "mapped_phophopeptides",
+                    "uuid": "d0fea028-2ea5-4862-8a92-c2088edfcbe1"
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+                {
+                    "label": "ppep_mapping_sqlite",
+                    "output_name": "mqppep_output_sqlite",
+                    "uuid": "eb996931-c548-4f3b-aaaa-39cc711df516"
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+                {
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+                    "output_name": "preproc_tab",
+                    "uuid": "c9410cf1-44a2-4aa6-b3df-06cef74f3a45"
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+                {
+                    "label": "preproc_sqlite",
+                    "output_name": "preproc_sqlite",
+                    "uuid": "4eb22cc3-5879-4625-89c0-e0fddb01a197"
+                },
+                {
+                    "label": "ppep_intensities",
+                    "output_name": "phosphoPepIntensities",
+                    "uuid": "c704fd66-5ac3-4779-ad40-536955cd81e3"
+                },
+                {
+                    "label": "enrichGraph_pdf",
+                    "output_name": "enrichGraph",
+                    "uuid": "5bf2a478-0431-4d32-84a9-7d46aad80ec5"
+                },
+                {
+                    "label": "quantData",
+                    "output_name": "quantData_tabular",
+                    "uuid": "cc922a75-6e72-4e60-add2-4b6ed8f73cdb"
+                }
+            ]
+        },
+        "8": {
+            "annotation": "Perform ANOVA. For imputing missing values, use median of non-missing values from the same treatment group.",
+            "content_id": "mqppep_anova",
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+            "id": 8,
+            "input_connections": {
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+                    "output_name": "output"
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+                "input_file": {
+                    "id": 7,
+                    "output_name": "preproc_tab"
+                }
+            },
+            "inputs": [],
+            "label": "MaxQuant Phosphopeptide ANOVA group-median imputed",
+            "name": "MaxQuant Phosphopeptide ANOVA",
+            "outputs": [
+                {
+                    "name": "imputed_data_file",
+                    "type": "tabular"
+                },
+                {
+                    "name": "report_file",
+                    "type": "pdf"
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+                "RenameDatasetActionimputed_data_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_group-mean-imputed_QN_LT"
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+                    "action_type": "RenameDatasetAction",
+                    "output_name": "imputed_data_file"
+                },
+                "RenameDatasetActionreport_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_group-mean-imputed_report (download/unzip to view)"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "report_file"
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+            },
+            "tool_id": "mqppep_anova",
+            "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"first_data_column\": \"Intensity\", \"imputation\": {\"imputation_method\": \"group-median\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"sample_grouping_regex\": \"(\\\\d+)\", \"sample_names_regex\": \"\\\\.(\\\\d+)[A-Z]$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+            "workflow_outputs": [
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+                    "label": "intensities_group-mean-imputed_QN_LT",
+                    "output_name": "imputed_data_file",
+                    "uuid": "169d677f-0acb-4c56-b057-21f4aaf2b920"
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+                {
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+                    "output_name": "report_file",
+                    "uuid": "25edae88-3bb6-4ec9-8b98-686fded7ed79"
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+        },
+        "9": {
+            "annotation": "Perform ANOVA. For imputing missing values, create random values.",
+            "content_id": "mqppep_anova",
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+            "id": 9,
+            "input_connections": {
+                "alpha_file": {
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+                "input_file": {
+                    "id": 7,
+                    "output_name": "preproc_tab"
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+            },
+            "inputs": [],
+            "label": "MaxQuant Phosphopeptide ANOVA randomly imputed",
+            "name": "MaxQuant Phosphopeptide ANOVA",
+            "outputs": [
+                {
+                    "name": "imputed_data_file",
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+}