Mercurial > repos > eschen42 > mqppep_anova

changeset 14:6679616d0c18 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 514e7b9b3a3730a5676821554449d5feb323eb9a"
author eschen42
date Tue, 22 Mar 2022 23:12:18 +0000
parents b41a077af3aa
children 2c5f1a2fe16a
files macros.xml mqppep_anova_script.Rmd workflow/ppenrich_suite_wf.ga
diffstat 3 files changed, 41 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Mar 22 20:47:40 2022 +0000
+++ b/macros.xml	Tue Mar 22 23:12:18 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.4</token>
+    <token name="@TOOL_VERSION@">0.1.5</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
--- a/mqppep_anova_script.Rmd	Tue Mar 22 20:47:40 2022 +0000
+++ b/mqppep_anova_script.Rmd	Tue Mar 22 23:12:18 2022 +0000
@@ -11,7 +11,7 @@
   inputFile: "test-data/test_input_for_anova.tabular"
   alphaFile: "test-data/alpha_levels.tabular"
   firstDataColumn: "Intensity"
-  imputationMethod: !r c("group-median", "median", "mean", "random")[1]
+  imputationMethod: !r c("group-median", "median", "mean", "random")[4]
   meanPercentile: 1
   sdPercentile: 1.0
   regexSampleNames: "\\.\\d+[A-Z]$"
--- a/workflow/ppenrich_suite_wf.ga	Tue Mar 22 20:47:40 2022 +0000
+++ b/workflow/ppenrich_suite_wf.ga	Tue Mar 22 23:12:18 2022 +0000
@@ -428,7 +428,13 @@
                 }
             },
             "tool_id": "mqppep_preproc",
-            "tool_state": "{\"collapseFunc\": \"sum\", \"intervalCol\": \"1\", \"localProbCutoff\": \"0.75\", \"merge_function\": \"sum\", \"networkin\": {\"__class__\": \"ConnectedValue\"}, \"p_sty_motifs\": {\"__class__\": \"ConnectedValue\"}, \"phosphoCol\": \"^Number of Phospho [(]STY[)]$\", \"phosphoSites\": {\"__class__\": \"ConnectedValue\"}, \"protein_fasta\": {\"__class__\": \"ConnectedValue\"}, \"psp_kinase_substrate\": {\"__class__\": \"ConnectedValue\"}, \"psp_regulatory_sites\": {\"__class__\": \"ConnectedValue\"}, \"pst_not_py\": \"true\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+
+
+
+
+
+
+            "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_not_py\": \"true\", \"pst_py_selector\": \"st\", \"species\": \"human\", \"startCol\": \"^Intensity[^_]\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": null,
             "type": "tool",
             "uuid": "1e983dba-edca-4aed-a589-49b1651b4a85",
@@ -524,6 +530,10 @@
                     "type": "tabular"
                 },
                 {
+                    "name": "imp_qn_lt_file",
+                    "type": "tabular"
+                },
+                {
                     "name": "report_file",
                     "type": "pdf"
                 }
@@ -544,6 +554,13 @@
                         "newname": "#{input_file}.intensities_group-mean-imputed_QN_LT"
                     },
                     "action_type": "RenameDatasetAction",
+                    "output_name": "imp_qn_lt_file"
+                },
+                "RenameDatasetActionimputed_data_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_group-mean-imputed"
+                    },
+                    "action_type": "RenameDatasetAction",
                     "output_name": "imputed_data_file"
                 },
                 "RenameDatasetActionreport_file": {
@@ -562,6 +579,11 @@
             "workflow_outputs": [
                 {
                     "label": "intensities_group-mean-imputed_QN_LT",
+                    "output_name": "imp_qn_lt_file",
+                    "uuid": "0e77a2e0-bd7a-4487-aaa6-ead2469509a2"
+                },
+                {
+                    "label": "intensities_group-mean-imputed",
                     "output_name": "imputed_data_file",
                     "uuid": "169d677f-0acb-4c56-b057-21f4aaf2b920"
                 },
@@ -596,6 +618,10 @@
                     "type": "tabular"
                 },
                 {
+                    "name": "imp_qn_lt_file",
+                    "type": "tabular"
+                },
+                {
                     "name": "report_file",
                     "type": "pdf"
                 }
@@ -616,6 +642,13 @@
                         "newname": "#{input_file}.intensities_randomly-imputed_QN_LT"
                     },
                     "action_type": "RenameDatasetAction",
+                    "output_name": "imp_qn_lt_file"
+                },
+                "RenameDatasetActionimputed_data_file": {
+                    "action_arguments": {
+                        "newname": "#{input_file}.intensities_randomly-imputed"
+                    },
+                    "action_type": "RenameDatasetAction",
                     "output_name": "imputed_data_file"
                 },
                 "RenameDatasetActionreport_file": {
@@ -640,6 +673,11 @@
                     "label": "intensities_randomly-imputed_report",
                     "output_name": "report_file",
                     "uuid": "d6701a61-357b-4a27-8154-ca41eb16d8a6"
+                },
+                {
+                    "label": "intensities_randomly-imputed_QN_LT",
+                    "output_name": "imp_qn_lt_file",
+                    "uuid": "637faf12-0d52-45b3-a318-40bfc7fcd4cb"
                 }
             ]
         }