--- a/interprophet.xml	Tue Jul 01 11:16:41 2014 -0400
+++ b/interprophet.xml	Thu Mar 26 19:55:19 2015 -0400
@@ -1,8 +1,9 @@
-<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1">
+<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
 	
 	<requirements>
-	    <requirement type="package" version="1.3">protk</requirement>
-	    <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement>
+         <container type="docker">iracooke/protk-1.4.1</container>
+	    <requirement type="package" version="1.4">protk</requirement>
+	    <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
 
 
@@ -22,35 +23,34 @@
 
 	$use_nsm 
 
-	--minprob $minprob
+	--p-thresh $p_thresh
+
+	--threads $threads
 
-	## Inputs.
-	${first_input}
-	#for $input_file in $input_files:
-	${input_file.additional_input}
-	#end for  	
+#for $pepxml_file in $pepxml_files:
+	${pepxml_file}
+#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="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="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" 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="blank" 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="blank" 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="blank" 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="blank" falsevalue="--no-nsm"/>
-	
-	<param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
+    <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" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
+    <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
   </outputs>
 
  <help>