diff msgfplus.xml @ 9:a26f5807eb85 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 75603eb19ef066d891fd906d7dd4b06f5498ca68

--- a/msgfplus.xml	Mon Oct 30 18:03:25 2017 -0400
+++ b/msgfplus.xml	Mon Dec 04 08:57:35 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="msgfplus" name="MS-GF+" version="0.4">
+<tool id="msgfplus" name="MS-GF+" version="0.5">
     <description>
         Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
     </description>
@@ -56,12 +56,15 @@
             -maxCharge $advanced.maxCharge
             -n $advanced.n
             -addFeatures $advanced.addFeatures
-        #if $tsvcheck
-            &&
-            msgf_plus
-              edu.ucsd.msjava.ui.MzIDToTsv
-              -i '$output_name'
-              -o output.tsv
+        #if $tsv == 'targets' or $tsv == 'decoys' 
+	    &&
+	    msgf_plus
+	        edu.ucsd.msjava.ui.MzIDToTsv
+	        -i '$output_name'
+	        -o output.tsv
+            #if $tsv == 'decoys'
+                -showDecoy 1
+            #end if
         #end if
         &&
         mv '$output_name' output
@@ -82,7 +85,10 @@
                       label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
               </when>
         </conditional>
-        <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
+        <param name="tsv" type="select" label="Output TSV as well?">
+            <option value="targets">Only target PSMs</option>
+            <option value="decoys">Both target and decoy PSMs</option>
+        </param>
         <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" />
         <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
         <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
@@ -246,7 +252,7 @@
             <param name="msgf_input|intype_selector" value="single" />
             <param name="msgf_input|s" value="input/201208-378803.mzML" />
             <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
-            <param name="tsvcheck" value="true" />
+            <param name="tsv" value="decoys" />
             <param name="tda" value="1" />
             <param name="ntt" value="1" />
             <param name="t" value="50" />