Mercurial > repos > galaxyp > flashlfq

diff flashlfq.xml @ 10:92c059f90d0e draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"
author galaxyp
date Tue, 07 Apr 2020 05:32:03 -0400
parents 878f6725c4f3
children
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--- a/flashlfq.xml	Thu Jan 09 02:52:23 2020 -0500
+++ b/flashlfq.xml	Tue Apr 07 05:32:03 2020 -0400
@@ -1,9 +1,12 @@
-<tool id="flashlfq" name="FlashLFQ" version="1.0.3.0">
+<tool id="flashlfq" name="FlashLFQ" version="1.0.3.1">
     <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
     <requirements>
         <requirement type="package" version="1.0.3">flashlfq</requirement>
     </requirements>
-    <command><![CDATA[
+    <stdio>
+        <regex match="Problem opening .mzML file" level="fatal" source="stdout" description="Proplem opening mzML file." />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
         #import re
         #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
         ln -s '${idt}' '${idt_path}' &&
@@ -45,7 +48,7 @@
                 #end if
             #end if
         #end if
-        --out out > logfile.txt
+        --out out | tee logfile.txt
     ]]></command>
     <inputs>
         <param argument="--idt" type="data" format="tabular" label="identification file"