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1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0">
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2
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.1</container>
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5 <requirement type="package" version="1.4">protk</requirement>
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6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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7 </requirements>
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8
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9
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10 <description>Combine Peptide Prophet results from multiple search engines</description>
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11
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12 <command>interprophet.rb --galaxy
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13
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14 -o interprophet_output.pep.xml
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15
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16 $use_nss
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17
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18 $use_nrs
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19
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20 $use_nse
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21
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22 $use_nsi
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23
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24 $use_nsm
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25
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26 --p-thresh $p_thresh
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27
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28 --threads $threads
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29
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30 #for $pepxml_file in $pepxml_files:
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31 ${pepxml_file}
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32 #end for
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33
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34 </command>
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35
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36
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37 <inputs>
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38
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39 <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"/>
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40
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41 <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"/>
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42 <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"/>
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43 <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"/>
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44 <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"/>
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45 <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"/>
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46
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47 <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"/>
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48
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49 <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>
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50
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51 </inputs>
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52 <outputs>
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53 <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/>
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54 </outputs>
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55
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56 <help>
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57
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58 **What it does**
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59
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60 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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61
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62 ----
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63
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64 **Citation**
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65
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66 If you use this tool please read and cite the paper describing iProphet
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67
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68 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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69
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70 </help>
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71
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72 </tool>
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