# HG changeset patch
# User galaxyp
# Date 1516921323 18000
# Node ID 279fbc8ad9929654ca29c654e8a4d8a5775ec6f2
# Parent  3b0c2e1927c1d6cc140d7493a72c7b9ae721325c
planemo upload for repository  https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de

diff -r 3b0c2e1927c1 -r 279fbc8ad992 flashlfq.xml
--- a/flashlfq.xml	Thu Jan 25 16:40:02 2018 -0500
+++ b/flashlfq.xml	Thu Jan 25 18:02:03 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="flashlfq" name="FlashLFQ" version="0.1.0">
+<tool id="flashlfq" name="FlashLFQ" version="0.1.99">
     <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
     <requirements>
         <requirement type="package" version="0.1.99">flashlfq</requirement>
@@ -6,18 +6,24 @@
     <command><![CDATA[
         #import re
         #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
-        mkdir spectrum_dir;
-        ln -s '${idt}' '${idt_path}';
+        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}' 'spectrum_dir/${input_name}';
+            ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
         #end for
-        FlashLFQ --idt '$idt_path' --rep spectrum_dir --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
@@ -90,7 +96,7 @@
     </tests>
     <help><![CDATA[
 
-**FlashLFQ** 
+**FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics.
 
 **Accepted command-line arguments:**