--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pout2mzid.xml	Sat Mar 04 20:36:03 2017 -0500
@@ -0,0 +1,94 @@
+<tool id="pout2mzid" name="Pout2mzid" version="0.3.03">
+    <description>add Percolator scoring to mzIdentML</description>
+    <requirements>
+	    <requirement type="package" version="0.3.03">pout2mzid</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+    #if $mzid.multifile == "true"
+        mkdir p2m_mzid_in &&
+        #set digits = "0" + str(len(str(len($mzid.mzids.keys()))))
+        #for $i, $fn in $enumerate($mzid.mzids.keys())
+            #set prefixnum = format($i, $digits)
+            ln -s '$mzid.mzids[$fn]' 'p2m_mzid_in/$fn' &&
+        #end for
+        ls p2m_mzid_in > infiles.txt &&
+        pout2mzid -p '$percout' -i p2m_mzid_in -f infiles.txt -o p2m_result -c _perco
+    
+    #else
+        ln -s '$mzid.mzidsingle' '$mzid.mzidsingle.display_name' &&
+        pout2mzid -p '$percout' -m '$mzid.mzidsingle.display_name'
+    #end if
+    
+    #if $targetdecoy == "decoy"
+        -d
+    #end if
+    #if $schemaskip
+        -v
+    #end if
+    #if $mzid.multifile == "false"
+        > '$output_single'
+    #end if
+    ]]></command>
+    <inputs>
+	    <param name="percout" type="data" format="percout" label="Percolator output"/>
+            <conditional name="mzid">
+                <param name="multifile" type="select" display="radio" label="Multiple mzIdentML files?">
+                    <option value="true">Yes</option>
+                    <option value="false" selected="true">No</option>
+                </param>
+                <when value="true">
+    	            <param name="mzids" type="data_collection" collection_type="list" format="mzid" label="mzIdentML from MSGF+" />
+                </when>
+                <when value="false">
+    	            <param name="mzidsingle" type="data" format="mzid" label="mzIdentML from MSGF+" />
+                </when>
+            </conditional>
+	    <param name="targetdecoy" type="select" display="radio" label="Which features to add to mzIdentML">
+		<option value="target" selected="true">Target</option>
+		<option value="decoy">Decoy</option>
+	    </param>
+	    <param name="schemaskip" type="boolean" label="Skip percolator schema validation?" />
+    </inputs>
+    <outputs>
+	    <data name="output_single" format="mzid">
+               <filter>mzid['multifile'] == "false"</filter>
+            </data>
+	    <collection name="output_multi" type="list">
+                <filter>mzid['multifile'] == "true"</filter>
+                <discover_datasets pattern="__designation__" ext="mzid" directory="p2m_result" />
+           </collection>
+            
+    </outputs>
+    <tests>
+        <test>
+            <param name="percout" value="percolatorOut.xml" />
+            <param name="mzid|multifile" value="false" />
+            <param name="mzid|mzidsingle" value="dataset_2.mzid" />
+            <param name="targetdecoy" value="target" />
+            <param name="schemaskip" value="true" />
+            <output name="output_single" value="target_ds2_withperco.mzid" />
+        </test>
+        <test>
+            <param name="percout" value="percolatorOut.xml" />
+            <param name="mzid|multifile" value="true" />
+            <param name="mzid|mzids">
+                <collection type="list">
+                    <element name="dataset_2.mzid" value="dataset_2.mzid" />
+                    <element name="dataset_3.mzid" value="dataset_2.mzid" />
+                </collection>
+            </param>
+            <param name="targetdecoy" value="target" />
+            <param name="schemaskip" value="true" />
+            <output_collection name="output_multi" type="list">
+                <element name="dataset_2_perco.mzid" value="target_ds2_withperco.mzid" />
+                <element name="dataset_3_perco.mzid" value="target_ds3_withperco.mzid" />
+            </output_collection>
+        </test>
+    </tests>
+    <help>Pout2Mzid extracts statistics from a percolator input file, and writes them to the mzIdentML file(s) that have been used
+	  to generate the percolator data. You may either pass multiple mzIdentML files in a list and one percolator file, or a single one.
+    </help>
+</tool>