--- a/workflow/ppenrich_suite_wf.ga	Tue Mar 22 23:12:18 2022 +0000
+++ b/workflow/ppenrich_suite_wf.ga	Sat Mar 26 02:27:12 2022 +0000
@@ -28,27 +28,155 @@
             "name": "Input dataset",
             "outputs": [],
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-                "right": 695,
-                "top": 264.5,
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-            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
+            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "21c3c29d-9e8c-4ece-b585-9e68fed7a93f",
+            "uuid": "78170155-4d6c-461b-a289-bcf0196b87db",
             "workflow_outputs": []
         },
         "1": {
+            "annotation": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)",
+                    "name": "Intensity-column pattern"
+                }
+            ],
+            "label": "Intensity-column pattern",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 443.9083480834961,
+                "height": 82.20000457763672,
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+            "tool_state": "{\"default\": \"^Intensity[^_]\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "b1a27840-417c-4e81-9fc3-7d3e3dee6753",
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Pattern extracting sample-names from names of columns that have peptide intensity data (PERL-compatible regular expression)",
+                    "name": "Sample-extraction pattern"
+                }
+            ],
+            "label": "Sample-extraction pattern",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 555.9083480834961,
+                "height": 82.20000457763672,
+                "left": 526.6583862304688,
+                "right": 726.6584014892578,
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+            "tool_state": "{\"default\": \"\\\\.\\\\d+[A-Z]$\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "05fe662c-b0a9-4ae7-8232-1b0a09261ac7",
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Pattern extracting sample-group from the sample-names that are extracted by 'Sample-extraction pattern' (PERL-compatible regular expression)",
+                    "name": "Group-extraction pattern"
+                }
+            ],
+            "label": "Group-extraction pattern",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 671.9083786010742,
+                "height": 82.20000457763672,
+                "left": 530.7000122070312,
+                "right": 730.7000274658203,
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+            "tool_state": "{\"default\": \"\\\\d+\", \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "55d4b63b-8863-4ee4-b504-4b436c6e9684",
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "THIS IS pST BY DEFAULT.  Change if your data are enriched for pY.",
+            "content_id": null,
+            "errors": null,
+            "id": 4,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "THIS IS pST BY DEFAULT.  Change if your data are enriched for pY.",
+                    "name": "enrichmentType"
+                }
+            ],
+            "label": "enrichmentType",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "bottom": 788.8083648681641,
+                "height": 61.80000305175781,
+                "left": 534.5750122070312,
+                "right": 734.5750274658203,
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+            "tool_state": "{\"restrictions\": [\"pST\", \"pY\"], \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "644c2a42-475d-4757-a58b-46d0d86323d3",
+            "workflow_outputs": []
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+        "5": {
             "annotation": "FASTA file of all human canonical isoforms, derived from Swiss-Prot (e.g., merge of https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz and https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz)",
             "content_id": null,
             "errors": null,
-            "id": 1,
+            "id": 5,
             "input_connections": {},
             "inputs": [
                 {
@@ -60,27 +188,27 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
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-                "right": 885,
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             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "5da7317c-4def-48f3-8eac-af95bd18b290",
+            "uuid": "c190d96f-c9ee-413b-ba19-75808b0eff55",
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         },
-        "2": {
+        "6": {
             "annotation": "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/)",
             "content_id": null,
             "errors": null,
-            "id": 2,
+            "id": 6,
             "input_connections": {},
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                 {
@@ -92,27 +220,27 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
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+            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
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             "type": "data_input",
-            "uuid": "2edff8de-4379-45e2-b6b9-6ed4706bbf00",
+            "uuid": "d2783d72-6639-4275-8726-6e32b956aaca",
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         },
-        "3": {
+        "7": {
             "annotation": "Derived from http://hprd.org/serine_motifs, http://hprd.org/tyrosine_motifs, and http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx",
             "content_id": null,
             "errors": null,
-            "id": 3,
+            "id": 7,
             "input_connections": {},
             "inputs": [
                 {
@@ -124,27 +252,27 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
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-                "left": 708,
-                "right": 908,
-                "top": 895.5,
-                "width": 200,
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+                "bottom": 1224.2084274291992,
+                "height": 82.20000457763672,
+                "left": 593.6000366210938,
+                "right": 793.6000518798828,
+                "top": 1142.0084228515625,
+                "width": 200.00001525878906,
+                "x": 593.6000366210938,
+                "y": 1142.0084228515625
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             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
+            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "86ebaaf2-b050-4eca-a88b-23a4c1af39f5",
+            "uuid": "e8c138eb-fb7d-4b4b-a5cc-25e000f555e1",
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         },
-        "4": {
+        "8": {
             "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,
+            "id": 8,
             "input_connections": {},
             "inputs": [
                 {
@@ -156,27 +284,27 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
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+                "bottom": 1354.6084289550781,
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+            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
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             "type": "data_input",
-            "uuid": "92f16705-a19c-4fb9-b278-3ae8e11f09d8",
+            "uuid": "d6aea327-574a-4657-ba6b-13fa973c182a",
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         },
-        "5": {
+        "9": {
             "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,
+            "id": 9,
             "input_connections": {},
             "inputs": [
                 {
@@ -188,27 +316,27 @@
             "name": "Input dataset",
             "outputs": [],
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+                "left": 594.5916748046875,
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             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}",
+            "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "5ab49d93-11e4-4e91-b30b-92269b319879",
+            "uuid": "1cda2502-f848-47d0-af07-d9997021b8c4",
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-        "6": {
+        "10": {
             "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,
+            "id": 10,
             "input_connections": {},
             "inputs": [
                 {
@@ -220,34 +348,34 @@
             "name": "Input dataset",
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-                "left": 727,
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             "type": "data_input",
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+            "uuid": "f59256bb-c823-48d6-923e-e54c6d04e155",
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         },
-        "7": {
-            "annotation": "",
+        "11": {
+            "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.",
             "content_id": "mqppep_preproc",
             "errors": null,
-            "id": 7,
+            "id": 11,
             "input_connections": {
                 "networkin": {
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                     "output_name": "output"
                 },
                 "p_sty_motifs": {
-                    "id": 3,
+                    "id": 7,
                     "output_name": "output"
                 },
                 "phosphoSites": {
@@ -255,20 +383,28 @@
                     "output_name": "output"
                 },
                 "protein_fasta": {
-                    "id": 1,
+                    "id": 5,
                     "output_name": "output"
                 },
                 "psp_kinase_substrate": {
+                    "id": 8,
+                    "output_name": "output"
+                },
+                "psp_regulatory_sites": {
+                    "id": 9,
+                    "output_name": "output"
+                },
+                "pst_py_selector": {
                     "id": 4,
                     "output_name": "output"
                 },
-                "psp_regulatory_sites": {
-                    "id": 5,
+                "startCol": {
+                    "id": 1,
                     "output_name": "output"
                 }
             },
             "inputs": [],
-            "label": null,
+            "label": "Preprocess MaxQuant Phospho (STY)Sites",
             "name": "MaxQuant Phosphopeptide Preprocessing",
             "outputs": [
                 {
@@ -325,16 +461,46 @@
                 }
             ],
             "position": {
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             },
             "post_job_actions": {
+                "HideDatasetActionfilteredData_tabular": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "filteredData_tabular"
+                },
+                "HideDatasetActionmapped_phophopeptides": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "mapped_phophopeptides"
+                },
+                "HideDatasetActionmelted_phophopeptide_map": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "melted_phophopeptide_map"
+                },
+                "HideDatasetActionmqppep_output_sqlite": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "mqppep_output_sqlite"
+                },
+                "HideDatasetActionpreproc_csv": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "preproc_csv"
+                },
+                "HideDatasetActionquantData_tabular": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "quantData_tabular"
+                },
                 "RenameDatasetActionenrichGraph": {
                     "action_arguments": {
                         "newname": "#{phosphoSites}.enrichGraph_pdf"
@@ -428,101 +594,73 @@
                 }
             },
             "tool_id": "mqppep_preproc",
-
-
-
-
-
-
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+            "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"pst_py_selector\": {\"__class__\": \"ConnectedValue\"}, \"species\": \"human\", \"startCol\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": null,
             "type": "tool",
-            "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85",
+            "uuid": "fc558352-b85e-438a-b94f-951f73768dfd",
             "workflow_outputs": [
                 {
-                    "label": "preproc_csv",
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                     "label": "locProbCutoffGraph_pdf",
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-                    "output_name": "melted_phophopeptide_map",
-                    "uuid": "878dc817-26a3-4061-9dd4-56e737b3c4f7"
+                    "uuid": "56f5f9b8-ae81-4743-abf8-1510b895eb2e"
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                 {
                     "label": "enrichGraph_svg",
                     "output_name": "enrichGraph_svg",
-                    "uuid": "4492366c-945e-492f-8381-1c97c4da2264"
+                    "uuid": "c4c8da47-9bad-4dc1-9205-374233e6c555"
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                     "label": "locProbCutoffGraph_svg",
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-                    "uuid": "06faf93c-5f04-4cb3-9e41-58e465f6180e"
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-                    "uuid": "76e2e268-f728-45f0-9973-793fbde0dd0a"
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-                    "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"
+                    "uuid": "40e1ef7c-a7ff-4ba4-8b8c-08be988d9b90"
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                 {
                     "label": "preproc_tab",
                     "output_name": "preproc_tab",
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+                    "uuid": "c53a5f0b-da40-4dc0-8e73-41f518b7844e"
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-                    "uuid": "4eb22cc3-5879-4625-89c0-e0fddb01a197"
+                    "uuid": "124ddcad-8fbd-489c-80ce-48cf2bc3c78c"
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                     "label": "ppep_intensities",
                     "output_name": "phosphoPepIntensities",
-                    "uuid": "c704fd66-5ac3-4779-ad40-536955cd81e3"
+                    "uuid": "25f871f9-6017-4209-ab8b-4551f3d34a79"
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                     "label": "enrichGraph_pdf",
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+                    "uuid": "e2d9f99e-23ec-4da8-aa0b-7ce4f59ea713"
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             "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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+                    "output_name": "output"
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             },
             "inputs": [],
-            "label": "MaxQuant Phosphopeptide ANOVA group-median imputed",
+            "label": "ANOVA group-median imputed",
             "name": "MaxQuant Phosphopeptide ANOVA",
             "outputs": [
                 {
@@ -539,17 +677,17 @@
                 }
             ],
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-                "RenameDatasetActionimputed_data_file": {
+                "RenameDatasetActionimp_qn_lt_file": {
                     "action_arguments": {
                         "newname": "#{input_file}.intensities_group-mean-imputed_QN_LT"
                     },
@@ -565,48 +703,56 @@
                 },
                 "RenameDatasetActionreport_file": {
                     "action_arguments": {
-                        "newname": "#{input_file}.intensities_group-mean-imputed_report (download/unzip to view)"
+                        "newname": "#{input_file}.intensities_group-mean-imputed_report"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "report_file"
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-            "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}",
+            "tool_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"imputation\": {\"imputation_method\": \"group-median\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"intensity_column_regex\": \"^Intensity[^_]\", \"sample_grouping_regex\": {\"__class__\": \"ConnectedValue\"}, \"sample_names_regex\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": null,
             "type": "tool",
-            "uuid": "ffa771c3-c52d-42a4-b78f-a60a39678792",
+            "uuid": "7002fe3a-bd4d-4d1d-9caf-1193606e3368",
             "workflow_outputs": [
                 {
                     "label": "intensities_group-mean-imputed_QN_LT",
                     "output_name": "imp_qn_lt_file",
-                    "uuid": "0e77a2e0-bd7a-4487-aaa6-ead2469509a2"
+                    "uuid": "61a62d74-1026-43ee-80f2-8c3905ebdeb5"
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                     "label": "intensities_group-mean-imputed",
                     "output_name": "imputed_data_file",
-                    "uuid": "169d677f-0acb-4c56-b057-21f4aaf2b920"
+                    "uuid": "c455ec37-f6c7-4abb-af6b-8ac6bea6d1a5"
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                     "label": "intensities_group-mean-imputed_report",
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-                    "uuid": "25edae88-3bb6-4ec9-8b98-686fded7ed79"
+                    "uuid": "9e138ec0-1248-4f4f-820f-6a8d05213662"
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             "annotation": "Perform ANOVA. For imputing missing values, create random values.",
             "content_id": "mqppep_anova",
             "errors": null,
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+            "id": 13,
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                     "output_name": "output"
                 },
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+                    "id": 11,
                     "output_name": "preproc_tab"
+                },
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+                    "output_name": "output"
+                },
+                "sample_names_regex": {
+                    "id": 2,
+                    "output_name": "output"
                 }
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             "inputs": [],
@@ -627,17 +773,17 @@
                 }
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-                "top": 1354,
-                "width": 200,
-                "x": 1617,
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+                "right": 1519.608413696289,
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+                "width": 200.00001525878906,
+                "x": 1319.6083984375,
+                "y": 1626.5084228515625
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             "post_job_actions": {
-                "RenameDatasetActionimputed_data_file": {
+                "RenameDatasetActionimp_qn_lt_file": {
                     "action_arguments": {
                         "newname": "#{input_file}.intensities_randomly-imputed_QN_LT"
                     },
@@ -653,31 +799,32 @@
                 },
                 "RenameDatasetActionreport_file": {
                     "action_arguments": {
-                        "newname": "#{input_file}.intensities_randomly-imputed_report (download/unzip to view)"
+                        "newname": "#{input_file}.intensities_randomly-imputed_report"
                     },
                     "action_type": "RenameDatasetAction",
                     "output_name": "report_file"
                 }
             },
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-            "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_state": "{\"alpha_file\": {\"__class__\": \"ConnectedValue\"}, \"imputation\": {\"imputation_method\": \"random\", \"__current_case__\": 3, \"meanPercentile\": \"1\", \"sdPercentile\": \"1.0\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"intensity_column_regex\": \"^Intensity[^_]\", \"sample_grouping_regex\": {\"__class__\": \"ConnectedValue\"}, \"sample_names_regex\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": null,
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+            "uuid": "b239a226-854c-4fbc-8955-cadd968f0704",
             "workflow_outputs": [
                 {
-                    "label": "intensities_randomly-imputed_QN_LT",
+                    "label": "intensities_randomly-imputed",
                     "output_name": "imputed_data_file",
-                    "uuid": "d70a3476-fb42-4533-831b-4fcb2bda74fc"
+                    "uuid": "8e403d6c-8f47-4f78-addd-da8923695135"
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+                    "uuid": "2c54a01e-ca12-4769-b370-cf137fe4b3f4"
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                     "output_name": "imp_qn_lt_file",
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+                    "uuid": "5fa4acc2-b82f-41e8-aedc-6efdc73f3d58"
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@@ -685,6 +832,6 @@
     "tags": [
         "ppenrich"
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-    "uuid": "445a0eb0-25c7-44c0-8259-a3346b01cbf3",
-    "version": 3
+    "uuid": "23c8a0f0-218f-4ba7-9470-ec826d16243a",
+    "version": 19
 }