# HG changeset patch
# User galaxyp
# Date 1512585973 18000
# Node ID d042eabcd6ec0c2633de711414351a4ad6b2300c
# Parent  a308025426194eacf3e73907c8493cc2863b3c38
Uploaded

diff -r a30802542619 -r d042eabcd6ec flashlfq.xml
--- a/flashlfq.xml	Wed Dec 06 09:04:50 2017 -0500
+++ b/flashlfq.xml	Wed Dec 06 13:46:13 2017 -0500
@@ -4,18 +4,32 @@
         <requirement type="package" version="0.1.99">flashlfq</requirement>
     </requirements>
     <command><![CDATA[
-        FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso
+        #import re
+        #set $idt_path = $re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1]) + ".psmtsv"
+        ## cp '${idt}' '${idt_path}';
+        ln -s '${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}';
+        #end for
+        FlashLFQ --idt $idt_path --rep `pwd` --ppm $ppm --iso $iso --nis $nis
         #if $intensity == 'integrate':
         --int true
         #end if
         #if $charge == 'precursor':
         --chg true
         #end if
+        $rmm $mbr
         --pau false
+        && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' 
+        && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
+        && cp *_FlashLFQ_QuantifiedModifiedSequences.tsv '$quantifiedModifiedSequences'
+        && cp *_FlashLFQ_QuantifiedPeaks.tsv '$quantifiedPeaks'
+        && cp *_FlashLFQ_QuantifiedProteins.tsv '$quantifiedProteins'
     ]]></command>
     <inputs>
         <param name="idt" type="data" format="tabular" label="identification file"/>
-        <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/>
+        <param name="peak_lists" type="data" format="mzml" multiple="true" label="spectrum files"/>
         <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/>
         <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/>
         <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/>
@@ -27,11 +41,13 @@
             <option value="all" selected="true">use all identification detected charge states</option>
             <option value="precursor">use precursor charge</option>
         </param>
-        <!--
-        -->
+        <param name="rmm" type="boolean" truevalue="--rmm true" falsevalue="--rmm false" checked="true" 
+            label="require observed monoisotopic mass peak"/>
+        <param name="mbr" type="boolean" truevalue="--mbr true" falsevalue="--mbr false" checked="false" 
+            label="match between runs"/>
     </inputs>
     <outputs>
-        <data name="log" format="text" label="${tool.name} on ${on_string}: Log" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" />
         <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" />
         <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" />
         <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" />
@@ -45,7 +61,7 @@
             <param name="iso" value="6"/>
             <output name="log">
                 <assert_contents>
-                    <has_text text="ppmTolerance = 10" />
+                    <has_text text="ppmTolerance = 12" />
                     <has_text text="isotopePpmTolerance = 6" />
                 </assert_contents>
             </output>
@@ -53,34 +69,25 @@
     </tests>
     <help><![CDATA[
 
-
+**FlashLFQ** 
 
 **Accepted command-line arguments:**
 
+::
+
     --idt [string | identification file path (TSV format)]
-    
     --raw [string | MS data file (.raw or .mzML)]
-    
     --rep [string | repository containing MS data files]
-    
     --ppm [double | monoisotopic ppm tolerance] (default = 10)
-    
     --iso [double | isotopic distribution tolerance in ppm] (default = 5)
-    
     --sil [boolean | silent mode; no console output] (default = false)
-    
     --pau [boolean | pause at end of run] (default = true)
-    
     --int [boolean | integrate chromatographic peak intensity instead of using 
           the apex intensity] (default = false)
-    
     --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks 
           for all charge states detected in the MS/MS identification file for each peptide] (default = false)
-   
     --mbr [bool|match between runs]
-
     --rmm [bool|require observed monoisotopic mass peak]
-   
     --nis [int|number of isotopes required to be observed]