# HG changeset patch
# User galaxyp
# Date 1509123853 14400
# Node ID b45ced785e01bbe7181de41977aacf421d54fbb8
# Parent  47408c5b15172dd1556e51352dad4b20b2c2a536
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 11837caf01413f2657b529b7cd7a4ec0960110fa

diff -r 47408c5b1517 -r b45ced785e01 msgfplus.xml
--- a/msgfplus.xml	Wed Sep 13 15:57:15 2017 -0400
+++ b/msgfplus.xml	Fri Oct 27 13:04:13 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="msgfplus" name="MS-GF+" version="0.3">
+<tool id="msgfplus" name="MS-GF+" version="0.3.1">
     <description>
         Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
     </description>
@@ -33,10 +33,11 @@
         #end for
 
         #for $mod in $custom_mods
-          echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
+          #set aa_nocomma = str($mod.aa_specificity).replace(",", "")
+          echo '${mod.formula_or_mass},${aa_nocomma},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
         #end for
 
-	msgf_plus
+        msgf_plus
             -s '$input_name'
             -d '$db_name'
             -thread \${GALAXY_SLOTS:-1}
@@ -55,31 +56,31 @@
             -maxCharge $advanced.maxCharge
             -n $advanced.n
             -addFeatures $advanced.addFeatures
-	#if $tsvcheck
-	    &&
-	    msgf_plus
-	        edu.ucsd.msjava.ui.MzIDToTsv
-	        -i '$output_name'
-	        -o output.tsv
-	#end if
+        #if $tsvcheck
+            &&
+            msgf_plus
+              edu.ucsd.msjava.ui.MzIDToTsv
+              -i '$output_name'
+              -o output.tsv
+        #end if
         &&
         mv '$output_name' output
 ]]>
     </command>
     <inputs>
         <conditional name="msgf_input">
-          <param name="intype_selector" type="select" label="Type of MSGF+ analysis">
-            <option value="single">Single database</option>
-            <option value="fractions">Prefractionated database</option>
-          </param>
-          <when value="single">
-            <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
-            <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
-          </when>
-          <when value="fractions">
-		  <param name="db_spectra" type="data_collection" collection_type="paired" 
-			  label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
-          </when>
+            <param name="intype_selector" type="select" label="Type of MSGF+ analysis">
+                <option value="single">Single database</option>
+                <option value="fractions">Prefractionated database</option>
+            </param>
+            <when value="single">
+                <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
+                <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
+              </when>
+              <when value="fractions">
+                  <param name="db_spectra" type="data_collection" collection_type="paired" 
+                      label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
+              </when>
         </conditional>
         <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
         <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
@@ -305,8 +306,15 @@
             <param name="custom_mods_1|fix_or_opt" value="opt" />
             <param name="custom_mods_1|position_specificity" value="any" />
             <param name="custom_mods_1|mod_name" value="cGMP" />
-
-            <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" />
+            
+            <output name="output">
+                <assert_contents>
+                    <has_text text="iTRAQ4plex" />
+                    <has_text text="pyro-Glu" />
+                    <has_text text="Gly-loss" />
+                    <has_text text="cGMP" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>