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1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0">
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2
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3 <requirements>
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4 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
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5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
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6 </requirements>
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7
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8
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9 <description>Combine Peptide Prophet results from multiple search engines</description>
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10
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11 <command interpreter="ruby">
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12
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13 interprophet_wrapper.rb $output $use_nss $use_nrs $use_nse $use_nsi $use_nsm --minprob $minprob
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14
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15
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16 ## Inputs.
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17 ${first_input}
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18 #for $input_file in $input_files:
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19 ${input_file.additional_input}
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20 #end for
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21
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22 </command>
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23
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24 <inputs>
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25
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26 <param name="first_input" 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"/>
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27
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28 <repeat name="input_files" title="Additional PepXML Input Files">
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29 <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/>
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30 </repeat>
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31
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32 <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--nonss"/>
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33 <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--nonrs"/>
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34 <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--nonse"/>
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35 <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--nonsi"/>
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36 <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--nonsm"/>
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37
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38 <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/>
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39
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40 </inputs>
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41 <outputs>
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42 <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/>
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43 </outputs>
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44
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45 <help>
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46
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47 **What it does**
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48
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49 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.
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50
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51 ----
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52
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53 **Citation**
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54
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55 If you use this tool please read and cite the paper describing iProphet
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56
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57 Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011).
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58
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59 </help>
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60
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61 </tool>
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