--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet.xml	Mon Jan 05 05:37:56 2015 -0500
@@ -0,0 +1,72 @@
+<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
+	
+	<requirements>
+            <container type="docker">simonalpha/protk:1.4.0</container>
+	    <requirement type="package" version="1.3">protk</requirement>
+	    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
+   </requirements>
+
+
+  <description>Combine Peptide Prophet results from multiple search engines</description>
+
+  <command>interprophet.rb --galaxy
+
+	-o interprophet_output.pep.xml
+
+	$use_nss 
+
+	$use_nrs 
+
+	$use_nse 
+
+	$use_nsi 
+
+	$use_nsm 
+
+	--p-thresh $p_thresh
+
+	--threads $threads
+
+#for $pepxml_file in $pepxml_files:
+	${pepxml_file}
+#end for	
+
+  </command>
+
+
+  <inputs>
+
+	<param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/>
+
+	<param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/>
+	<param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/>
+	<param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/>
+	<param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/>
+	<param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/>
+	
+    <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/>
+
+	<param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
+		
+  </inputs>
+  <outputs>
+    <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].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>