<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
	
	<requirements>
         <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>


  <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>