--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/percolator_converters.xml	Fri Mar 10 03:20:52 2017 -0500
@@ -0,0 +1,121 @@
+<tool id="percolator_input_converters" name="Search engine output to Pin converter" version="3.1">
+    <description>to create Percolator input files</description>
+    <requirements>
+        <requirement type="package" version="3.1">percolator</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+             mkdir target && mkdir decoy &&
+             
+             #if $mzids.inputtype == "multi"
+                 #for $key in $mzids.target.keys()
+                     ln -s '$mzids.target[$key]' 'target/$key' &&
+                     echo 'target/$key' >> targetmeta &&
+                 #end for
+                 #for $key in $mzids.decoy.keys()
+                     ln -s '$mzids.decoy[$key]' 'decoy/$key' &&
+                     echo 'decoy/$key' >> decoymeta &&
+                 #end for
+                 $searchengine -o $pinout -e $enzyme
+                 #if $matches
+                     -m $matches
+                 #end if
+                 $aafreq $ptm $pngase $isotope targetmeta decoymeta
+             
+             #else
+                 ln -s '$mzids.target' 'target/$target.display_name' &&
+                 ln -s '$mzids.decoy' 'decoy/$decoy.display_name' &&
+                 $searchengine -o $pinout -e $enzyme
+                 #if $matches
+                     -m $matches
+                 #end if
+                 $aafreq $ptm $pngase $isotope
+                 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name'
+             #end if
+    ]]></command>
+    <inputs>
+        <param name="searchengine" type="select" label="Search engine used">
+            <option value="msgf2pin">MSGF+ (mzIdentML)</option>
+            <option value="tandem2pin">X!Tandem (tandem)</option>
+            <option value="sqt2pin">Crux (SQT output)</option>
+        </param>
+        <conditional name="mzids">
+            <param name="inputtype" type="select" display="radio">
+                <option value="single">Single mzIdentML</option>
+                <option value="multi">Multiple mzIdentMLs</option>
+            </param>
+	    <when value="single">
+                <param name="target" type="data" format="mzid" label="Target MSGF+ results" />
+                <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" />
+            </when>
+	    <when value="multi">
+                <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" />
+                <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" />
+            </when>
+        </conditional>
+        <param name="enzyme" type="select" label="Enzyme used">
+          <option value="trypsin">trypsin</option>
+          <option value="no_enzyme">no enzyme</option>
+          <option value="elastase">elastase</option>
+          <option value="pepsin">pepsin</option>
+          <option value="proteinasek">proteinase K</option>
+          <option value="thermolysin">thermolysin</option>
+          <option value="chymotrypsin">chymotrypsin</option>
+          <option value="lys-n">lys-N</option>
+          <option value="lys-c">lys-C</option>
+          <option value="arg-c">arg-C</option>
+          <option value="asp-n">asp-N</option>
+          <option value="glu-c">glu-C</option>
+        </param>
+        <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
+	<param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
+        <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
+        <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
+        <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data format="percin" name="pinout"/>
+    </outputs>
+    <tests>
+        <test>
+          <param name="mzids|inputtype" value="single" />
+          <param name="mzids|target" value="target.mzid" />
+          <param name="mzids|decoy" value="decoy.mzid" />
+          <param name="ptm" value="true"/>
+          <param name="matches" value="1"/>
+          <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
+        </test>
+        <test>
+          <param name="mzids|inputtype" value="multi" />
+          <param name="mzids|target">
+                <collection type="list">
+                    <element name="target1" value="target.mzid" />
+                    <element name="target2" value="target.mzid" />
+                </collection>
+          </param>
+          <param name="mzids|decoy">
+                <collection type="list">
+                    <element name="decoy1" value="decoy.mzid" />
+                    <element name="decoy2" value="decoy.mzid" />
+                </collection>
+          </param>
+          <param name="ptm" value="true"/>
+          <param name="matches" value="1"/>
+          <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" />
+        </test>
+    </tests>
+    <help>
+The percolator converter msgf2pin converts mzIdentML to input for percolator.
+Target and decoy inputs are MzIdentML-files of MS-GF+ from
+separate target and decoy searches. Internal MS-GF+ target/decoy
+analysis should be turned off, and the addFeatures options turned on.
+Multiple MzIdentML-files can be merged by passing lists of these.
+For successful results, the different runs should be generated under 
+similar conditions.
+    </help>
+    <citations>
+        <citation type="doi">10.1021/pr400937n</citation>
+    </citations>
+</tool>