<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
    <description>Combine Peptide Prophet results from multiple search engines</description>
    <requirements>
         <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    <command>
<![CDATA[
        export XML_ONLY="true";

        interprophet.rb --galaxy
        #if str( $input_type.type ) == "files":
            #for $pepxml_file in $input_type.pepxml_files:
                ${pepxml_file}
            #end for
        #else
            #for $list_item in $input_type.pepxml_list:
                ${list_item}
            #end for
            #for $extra_list_holder in $input_type.extra_pepxml_lists:
                #for $list_item in $extra_list_holder.extra_list:
                    ${list_item}
                #end for
            #end for
        #end if

            -o interprophet_output.pep.xml
            $use_nss
            $use_nrs
            $use_nse
            $use_nsi
            $use_nsm
            --p-thresh $p_thresh
            --threads "\${GALAXY_SLOTS:-12}"

]]>
    </command>
    <inputs>

        <conditional name="input_type">
            <param name="type" type="select" label="Input Type">
                <option value="files" selected="true">Datasets</option>
                <option value="collections">Collections</option>
            </param>
            <when value="files">
                <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"/>
            </when>
            <when value="collections">
                <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" 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="extra_pepxml_lists" title="Additional PepXML Collections" >
                    <param name="extra_list" type="data_collection" multiple="true" collection_type="list" 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>
            </when>
        </conditional>

        <!-- <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"/>

    </inputs>
    <outputs>
        <data format="interprophet_pepxml" name="output" 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>