<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1">
    <description>Calculate Protein Prophet statistics on search results</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>
        protein_prophet.rb
            --galaxy 
            
            #for $input_file in $input_files:
                ${input_file}
            #end for
            
            -o protein_prophet_results.prot.xml
            -r

            $iproph
            $nooccam
            $groupwts
            $normprotlen
            $logprobs
            $confem
            $allpeps
            $unmapped
            $instances
            $delude
          --minprob=$minprob
          --minindep=$minindep
    </command>
    <inputs>
        <param name="input_files" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="true" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/>

        <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
        <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/>
        <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/>
        <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
        <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
        <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
        <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
        <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
        <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
        <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>

        <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
        <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
    </inputs>
    <outputs>
        <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/>
    </outputs>


<!--NOPLOT: do not generate plot png file
        NOOCCAM: non-conservative maximum protein list
        GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)   
        NORMPROTLEN: Normalize NSP using Protein Length
        LOGPROBS: Use the log of the probabilities in the Confidence calculations
        CONFEM: Use the EM to compute probability given the confidence 
        ALLPEPS: Consider all possible peptides in the database in the confidence model
        UNMAPPED: Report results for UNMAPPED proteins
        INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
        DELUDE: do NOT use peptide degeneracy information when assessing proteins
        
        MINPROB: peptideProphet probabilty threshold (default=0.05) 
        MININDEP: minimum percentage of independent peptides required for a protein (default=0) 
-->

    <help>

**What it does**

Given a set of peptide assignments from MS/MS spectra in the form of a pepXML file, this tool estimates probabilities at the protein level.  As output, the tool produces a protXML file, which contains proteins along with the estimated probabilities that those proteins were present.  Probabilities are estimated using a statistical model based on the number of peptides corresponding to that protein and the confidence that each of those peptides were assigned correctly.  It takes account of the fact that peptides may correspond to more than one protein. 

----

**Citation**

If you use this tool please read and cite the paper describing the statistical model implemented by Protein Prophet

Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003).


    </help>
</tool>