comparison interprophet.xml @ 15:0746a2ae9e04 draft

planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

14:d90c8bc10a9c

<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. 

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>

15:0746a2ae9e04

<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[
        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. 

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>