--- a/percolator.xml	Sat Mar 04 20:36:03 2017 -0500
+++ b/percolator.xml	Fri Mar 10 03:20:52 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="percolator" name="Percolator" version="3.0.1">
+<tool id="percolator" name="Percolator" version="3.1.0">
     <description>accurate peptide identification</description>
     <requirements>
-        <requirement type="package" version="3.0">percolator</requirement>
+        <requirement type="package" version="3.1">percolator</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"/>
@@ -13,6 +13,7 @@
     #else
         -J '$percoout'
     #end if
+    $tdmethod
     #if $cpos
         -p $cpos
     #end if
@@ -37,18 +38,22 @@
     $quickval $unitnorm $override $onlypsms
     </command>
     <inputs>
-        <param name="output_type" label="What filetype to output" type="select" display="radio">
-            <option value="xml" selected="true">percolator XML (for further processing)</option>
-	    <option value="tsv">Tab-separated</option>
+        <param name="output_type" label="What to output" type="select" display="radio">
+            <option value="xml" selected="true">Percolator output (XML)</option>
+	    <option value="tsv">Computed features of input (Tab separated)</option>
         </param>
         <param name="input" type="data" format="percin" label="Percolator input data" />
+        <param name="tdmethod" type="select" label="Target decoy method">
+            <option value="-y" selected="true">Mix-max</option>
+	    <option value="-Y">Target-decoy competition (also good when unequal amounts of target/decoy PSMs)</option>
+        </param>
         <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" />
         <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" />
         <param name="trainfdr" label="FDR threshold to define positive examples" type="float" optional="true" help="Set by cross validation if 0."/>
         <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" />
         <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" />
         <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/>
-        <param name="default_direction" label="Most informative feature given as feature number" type="integer" optional="true" />
+        <param name="default_direction" label="Most informative feature given as feature name." help="Can be negated to indicate lower value=better, e.g -featureName" type="text" optional="true" />
         <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/>
         <param name="override" label="Override error check?" help="and no fallback on default score vector in case of suspect score vector" type="boolean" truevalue="-O" falsevalue=""/>
         <param name="seed" label="Seed of random number generator" type="integer" optional="true" />
@@ -70,8 +75,25 @@
         </test>
         <test>
             <param name="input" value="percolatorTab" />
+            <param name="output_type" value="xml" />
+            <param name="tdmethod" value="-Y" />
+            <param name="cpos" value="0.00001" />
+            <param name="cneg" value="0.00001" />
+            <param name="trainfdr" value="0.1" />
+            <param name="testfdr" value="0.1" />
+            <param name="maxiter" value="5" />
+            <param name="quickval" value="-x" />
+            <param name="default_direction" value="RawScore" />
+            <param name="unitnorm" value="-u" />
+            <param name="override" value="-O" />
+            <param name="seed" value="2" />
+            <param name="onlypsms" value="-U" />
+            <output name="percoout" value="percolatorOut_alloptions.xml" lines_diff="2" />
+        </test>
+        <test>
+            <param name="input" value="percolatorTab" />
             <param name="output_type" value="tsv" />
-            <output name="percoout" value="percolatorOut.txt" />
+            <output name="percoout" value="percolatorOut.txt" lines_diff="1" />
         </test>
     </tests>
     <help>The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications.