Mercurial > repos > galaxyp > flashlfq

diff flashlfq.xml @ 2:e70198847b2a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 38eecdb36b6b505afcdd99de7351eed9c3729843
author galaxyp
date Thu, 25 Jan 2018 20:37:09 -0500
parents 1e2fc34b1f20
children ff1148892ce3
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--- a/flashlfq.xml	Thu Jan 25 18:02:19 2018 -0500
+++ b/flashlfq.xml	Thu Jan 25 20:37:09 2018 -0500
@@ -31,7 +31,8 @@
         && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
         && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
         && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
-        && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins'
+        ## create issue for FlashLFQ to name column headers correctly
+        && grep -v '^test$' *_FlashLFQ_QuantifiedProteins.tsv > '$quantifiedProteins'
     ]]></command>
     <inputs>
         <param name="idt" type="data" format="tabular" label="identification file" 
@@ -76,7 +77,7 @@
         <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv">
             <actions>
                 <action name="column_names" type="metadata" 
-                 default="Protein"/>
+                 default="Protein,${','.join([i.name for i in $peak_lists])}"/>
             </actions>
         </data>
     </outputs>