--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet.xml	Mon Jul 23 00:20:58 2012 -0400
@@ -0,0 +1,55 @@
+<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0">
+	<requirements><requirement type="package">protk</requirement></requirements>
+  <description>Combine Peptide Prophet results from multiple search engines</description>
+
+  <command interpreter="ruby">
+
+	interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob
+
+
+	## Inputs.
+	${first_input}
+	#for $input_file in $input_files:
+	${input_file.additional_input}
+	#end for  	
+
+  </command>
+
+  <inputs>
+
+	<param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> 	
+		
+	<repeat name="input_files" title="Additional PepXML Input Files">
+		<param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
+	</repeat>
+	
+	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/>
+	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/>
+	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/>
+	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/>
+	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/>
+	
+	<param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
+		
+  </inputs>
+  <outputs>
+    <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
+  </outputs>
+
+ <help>
+
+**What it does**
+
+Takes a set of pepXML files (possibly generated using different search engines) and calculates updated identification probabilities for each peptide.  The updated probabilities are based on a statistical model that combines evidence from identifications across all of the input files, spectra, modified states and charge states. 
+
+----
+
+**Citation**
+
+If you use this tool please read and cite the paper describing iProphet
+
+Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
+
+  </help>
+
+</tool>