diff msgfplus.xml @ 3:b4ccaf21855d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7

--- a/msgfplus.xml	Wed Dec 07 16:43:17 2016 -0500
+++ b/msgfplus.xml	Thu Jan 12 15:25:02 2017 -0500
@@ -4,7 +4,6 @@
     </description>
     <requirements>
         <requirement type="package" version="2016.10.26">msgf_plus</requirement>
-        <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
@@ -56,6 +55,13 @@
             -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
         &&
         mv '$output_name' output
 ]]>
@@ -75,6 +81,7 @@
 			  label="Collection: Pairs of FASTA database (forward) and spectra (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" />
         <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">
@@ -217,12 +224,15 @@
     </inputs>
     <outputs>
         <data name="output" format="mzid" from_work_dir="output" />
+        <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" >
+          <filter>tsvcheck</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-	    <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="msgf_input|intype_selector" value="single" />
+            <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" />
+            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" />
             <param name="tda" value="1" />
             <param name="ntt" value="1" />
             <param name="t" value="50" />
@@ -232,21 +242,39 @@
             <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
         </test>
         <test>
-	    <param name="msgf_input.intype_selector" value="fractions" />
-            <param name="msgf_input.db_spectra.forward" value="input/201208-378803.mzML" />
-            <param name="msgf_input.db_spectra.reverse" value="input/cow.protein.PRG2012-subset.fasta" />
+            <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="tda" value="1" />
+            <param name="ntt" value="1" />
+            <param name="t" value="50" />
+            <param name="precursor_ion_tol_units" value="ppm" />
+            <param name="common_fixed_modifications" value="" />
+            <param name="common_variable_modifications" value="" />
+            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
+            <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" />
+        </test>
+        <test>
+            <param name="msgf_input|intype_selector" value="fractions" />
+            <param name="msgf_input|db_spectra">
+                <collection type="paired">
+                    <element name="forward" value="input/201208-378803.mzML" />
+                    <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" />
+                </collection>
+            </param>
             <param name="tda" value="1" />
             <param name="ntt" value="1" />
             <param name="t" value="50" />
             <param name="precursor_ion_tol_units" value="ppm" />            
             <param name="common_fixed_modifications" value="" />
             <param name="common_variable_modifications" value="" />
-            <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
+            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
         </test>
         <test>
-	    <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="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="tda" value="1" />
             <param name="t" value="0.02" />
             <param name="precursor_ion_tol_units" value="Da" />