# HG changeset patch
# User galaxyp
# Date 1516921339 18000
# Node ID 1e2fc34b1f20ef82f29689d9178420d6c7c98375
# Parent  6d3560a3a548da9bcfed232863c21a4c650a035c
planemo upload for repository  https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de

diff -r 6d3560a3a548 -r 1e2fc34b1f20 flashlfq.xml
--- a/flashlfq.xml	Thu Jan 25 16:10:58 2018 -0500
+++ b/flashlfq.xml	Thu Jan 25 18:02:19 2018 -0500
@@ -7,14 +7,15 @@
         #import re
         #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
         ln -s '${idt}' '${idt_path}' &&
+        mkdir spectrum_dir &&
         #for $peak_list in $peak_lists:
             #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
-            ln -s '${peak_list}' '${input_name}' &&
+            ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
         #end for
 
         FlashLFQ 
         --idt '$idt_path'
-        --rep `pwd`
+        --rep spectrum_dir
         --ppm $ppm
         --iso $iso
         --nis $nis