# HG changeset patch
# User galaxyp
# Date 1628680252 0
# Node ID 439418d3eb817f9343c6eaacecf5e4843a3c2477
# Parent  1a36fd860cdf0d23995d93b2641de63ecfb14287
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455"

diff -r 1a36fd860cdf -r 439418d3eb81 msstatstmt.xml
--- a/msstatstmt.xml	Mon Jul 26 20:20:53 2021 +0000
+++ b/msstatstmt.xml	Wed Aug 11 11:10:52 2021 +0000
@@ -564,7 +564,7 @@
 
 **Notes**
 
-- MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required.
+- MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required, which has to be in the format 'channel.X' with X being the channel number..
 
     ::
 
@@ -582,13 +582,13 @@
     #> 4               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
     #> 5               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
     #> 6               3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3       3
-    #>   TechRepMixture   Run Channel BioReplicate Condition Intensity
-    #> 1            3_3 3_3_3       1           21   Long_HF        NA
-    #> 2            3_3 3_3_3       2           22      Norm  1068.580
-    #> 3            3_3 3_3_3       3           23    Long_M  1508.330
-    #> 4            3_3 3_3_3       4           24   Long_HF        NA
-    #> 5            3_3 3_3_3       5           25   Long_LF  1580.951
-    #> 6            3_3 3_3_3       6           26   Long_HF  1820.072
+    #>   TechRepMixture   Run         Channel BioReplicate Condition Intensity
+    #> 1            3_3 3_3_3       channel.1           21   Long_HF        NA
+    #> 2            3_3 3_3_3       channel.2           22      Norm  1068.580
+    #> 3            3_3 3_3_3       channel.3           23    Long_M  1508.330
+    #> 4            3_3 3_3_3       channel.4           24   Long_HF        NA
+    #> 5            3_3 3_3_3       channel.5           25   Long_LF  1580.951
+    #> 6            3_3 3_3_3       channel.6           26   Long_HF  1820.072
 
     For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_
 
@@ -619,6 +619,7 @@
 For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_
 ]]>
     </help>
+
     <citations>
         <citation type="doi">10.1074/mcp.ra120.002105</citation>
     </citations>