# HG changeset patch
# User galaxyp
# Date 1586251923 14400
# Node ID 92c059f90d0e04851238ee886033e78be78c11ea
# Parent  878f6725c4f3ca785202614b1eca8daa957be453
"planemo upload for repository  https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a72ed1b1e61e0f948dc36b220d2746dc6f06bccf"

diff -r 878f6725c4f3 -r 92c059f90d0e flashlfq.xml
--- 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"