Mercurial > repos > iracooke > tpp_prophets

annotate interprophet.xml @ 16:1b86e378de37 draft

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Fix tabular outputs. Export XML_ONLY variable
author iracooke
date Mon, 26 Oct 2015 20:40:34 -0400
parents 0746a2ae9e04
children
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1 <tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1">
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2 <description>Combine Peptide Prophet results from multiple search engines</description>
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3 <requirements>
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4 <container type="docker">iracooke/protk-1.4.3</container>
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5 <requirement type="package" version="1.4.3">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 <command>
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9 <![CDATA[
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10 export XML_ONLY="true";
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12 interprophet.rb --galaxy
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13 #if str( $input_type.type ) == "files":
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14 #for $pepxml_file in $input_type.pepxml_files:
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15 ${pepxml_file}
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16 #end for
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17 #else
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18 #for $list_item in $input_type.pepxml_list:
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19 ${list_item}
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20 #end for
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21 #for $extra_list_holder in $input_type.extra_pepxml_lists:
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22 #for $list_item in $extra_list_holder.extra_list:
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23 ${list_item}
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24 #end for
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25 #end for
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26 #end if
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28 -o interprophet_output.pep.xml
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29 $use_nss
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30 $use_nrs
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31 $use_nse
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32 $use_nsi
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33 $use_nsm
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34 --p-thresh $p_thresh
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35 --threads "\${GALAXY_SLOTS:-12}"
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36
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37 ]]>
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38 </command>
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39 <inputs>
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40
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41 <conditional name="input_type">
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42 <param name="type" type="select" label="Input Type">
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43 <option value="files" selected="true">Datasets</option>
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44 <option value="collections">Collections</option>
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45 </param>
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46 <when value="files">
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47 <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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48 </when>
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49 <when value="collections">
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50 <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"/>
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51 <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" >
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52 <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"/>
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53 </repeat>
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54 </when>
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55 </conditional>
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56
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57 <!-- <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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59 <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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60 <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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61 <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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62 <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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63 <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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64 <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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65
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66 </inputs>
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67 <outputs>
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68 <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/>
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69 </outputs>
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70 <help>
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71
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72 **What it does**
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73
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74 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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75
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76 ----
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77
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78 **Citation**
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80 If you use this tool please read and cite the paper describing iProphet
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81
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82 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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83
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84 </help>
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85 </tool>