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<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0">
	<requirements><requirement type="package">protk</requirement></requirements>
  <description>Calculate Protein Prophet statistics on search results</description>


<!-- Note .. the input file is assumed to be the first argument -->
  <command interpreter="ruby">protein_prophet_wrapper.rb $output $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command>
  <inputs>
	
    <param name="input_file" type="data" format="pepxml" multiple="false" 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" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" 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>
	Run Peptide Prophet
  </help>

</tool>