# HG changeset patch
# User galaxyp
# Date 1516916402 18000
# Node ID 3b0c2e1927c1d6cc140d7493a72c7b9ae721325c
# Parent  597199e75dcc126fac020a52bfad12d8680e0ad5
planemo upload for repository  https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit 8b11559f7c02a4a686af1086740795ace14d077d-dirty

diff -r 597199e75dcc -r 3b0c2e1927c1 flashlfq.xml
--- a/flashlfq.xml	Thu Jan 25 16:10:39 2018 -0500
+++ b/flashlfq.xml	Thu Jan 25 16:40:02 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="flashlfq" name="FlashLFQ" version="0.1.99">
+<tool id="flashlfq" name="FlashLFQ" version="0.1.0">
     <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
     <requirements>
         <requirement type="package" version="0.1.99">flashlfq</requirement>
@@ -6,23 +6,18 @@
     <command><![CDATA[
         #import re
         #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
-        ln -s '${idt}' '${idt_path}' &&
+        mkdir spectrum_dir;
+        ln -s '${idt}' '${idt_path}';
         #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`
-        --ppm $ppm
-        --iso $iso
-        --nis $nis
+        FlashLFQ --idt '$idt_path' --rep spectrum_dir --ppm $ppm --iso $iso --nis $nis
         #if $intensity == 'integrate':
-            --int true
+        --int true
         #end if
         #if $charge == 'precursor':
-            --chg true
+        --chg true
         #end if
         $rmm $mbr
         --pau false
@@ -95,7 +90,7 @@
     </tests>
     <help><![CDATA[
 
-**FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics.
+**FlashLFQ** 
 
 **Accepted command-line arguments:**