--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteinpilot_tabular.xml	Wed Dec 19 00:22:55 2012 -0500
@@ -0,0 +1,41 @@
+<tool id="proteinpilot_tabular" version="0.1" name="Convert ProteinPilot Group to Tabular">
+  <description></description>
+  <command>
+    #if $quant.use
+    #set $denom = $quant.type
+    #else
+    #set $denom = ""
+    #end if
+    group2xml.exe ${type} $input $output $denom
+  </command>
+  <inputs>
+    <param format="group" name="input" type="data" label="ProteinPilot Group Data" help=""/>
+    <param name="type" type="select" label="Summary Type">
+      <option value="PROTEIN">Protein</option>
+      <option value="PEPTIDE">Peptide</option>
+    </param>
+    <conditional name="quant">
+      <param name="use" type="boolean" label="Include quantation results" truevalue="true" falsevalue="false" />
+      <when value="true">
+        <param name="type" type="select" label="Denominator">
+          <option value="IT113">113</option>
+          <option value="IT114" selected="true">114</option>
+          <option value="IT115">115</option>
+          <option value="IT116">116</option>
+          <option value="IT117">117</option>
+          <option value="IT118">118</option>
+          <option value="IT119">119</option>
+          <option value="IT121">121</option>
+          <option value="Light">Light</option>
+          <option value="Heavy">Heavy</option>
+          <option value="Medium">Medium</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="${type} report for ${on_string}"/>
+  </outputs>
+  <help>
+  </help>
+</tool>