# HG changeset patch
# User galaxyp
# Date 1597421954 14400
# Node ID 52ac6fde9a5bd7f5f9c7f2d9a20050eedc8b34f8
# Parent  3e2606fa85bfc7c37285f66b470a221d162d4b01
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats commit 414edbbd89f9bc83b81289e409c9b688c8c1e40f"

diff -r 3e2606fa85bf -r 52ac6fde9a5b msstats.xml
--- a/msstats.xml	Sat Jul 25 14:49:56 2020 -0400
+++ b/msstats.xml	Fri Aug 14 12:19:14 2020 -0400
@@ -232,7 +232,7 @@
 
   #if 'volcanoplot' in $group.select_outputs
 \# volcano plot
-groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot',
+groupComparisonPlots(data = comparisons\$ComparisonResult, type = 'VolcanoPlot',ProteinName=FALSE,
                      width=5, height=5, address="MSStats_group_")
   #end if
 
@@ -704,9 +704,9 @@
 
 - Annotations as tabular file are needed for all input options except MSstats format
 
-    - 4 columns: Filename, Condition, Bioreplicate, Run; additional 5th column only for MaxQuant: Isotopelabeltype
+    - 4 columns with exactly these headers: Raw.file, Condition, BioReplicate, Run; additional 5th column only for MaxQuant: IsotopeLabelType
     
-        - Filename: the file name has to be exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML)
+        - Raw.file: File name that has to match exactly as it appears in the other input files (e.g. S1207.raw.thermo; in/AA12_mzML.mzML)
         - all other columns: see description above for MSstats format columns
 
 - Comparison matrix as tabular file