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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDFileConverter" name="IDFileConverter" version="1.12.0">
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3 <description>Converts identification engine file formats.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDFileConverter</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IDFileConverter
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -out_type ${param_out_type}
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15 -mz_file ${param_mz_file}
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16 -mz_name ${param_mz_name}
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17 ${param_use_precursor_data}
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18 ${param_peptideprophet_analyzed}
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19 -threads \${GALAXY_SLOTS:-24}
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20 #if $adv_opts.adv_opts_selector=='advanced':
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21 ${adv_opts.param_ignore_proteins_per_peptide}
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22 -scan_regex ${adv_opts.param_scan_regex}
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="param_in" type="data" format="pepXML,idXML" optional="False" label="Input file or directory containing the output of the search engine.#br#Sequest: Directory containing the .out files#br#pepXML: Single pepXML file.#br#protXML: Single protXML file.#br#mascotXML: Single Mascot XML file.#br#omssaXML: Single OMSSA XML file.#br#XTandem: Single XML file.#br#idXML: Single idXML file.#br#" help="(-in)"/>
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27 <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content#br#" help="(-out_type)">
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28 <option value="idXML">idXML</option>
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29 <option value="mzid">mzid</option>
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30 <option value="pepXML">pepXML</option>
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31 <option value="FASTA">FASTA</option>
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32 </param>
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33 <param name="param_mz_file" type="data" format="mzML,mzXML" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file)"/>
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34 <param name="param_mz_name" type="text" size="20" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'." help="(-mz_name)"/>
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35 <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data true" falsevalue="-use_precursor_data false" checked="false" optional="True" label="[pepXML only] Use precursor RTs (and m/z values) from 'mz_file' for the generated peptide identifications, instead of the RTs of MS2 spectra." help="(-use_precursor_data)"/>
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36 <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed true" falsevalue="-peptideprophet_analyzed false" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results." help="(-peptideprophet_analyzed)"/>
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37 <expand macro="advanced_options">
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38 <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide true" falsevalue="-ignore_proteins_per_peptide false" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column,#br#but do not list extra references in subsequent lines (try -debug 3 or 4)" help="(-ignore_proteins_per_peptide)"/>
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39 <param name="param_scan_regex" type="text" size="20" label="[mascotXML only] Regular expression used to extract the scan number or retention time. See documentation for details." help="(-scan_regex)"/>
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40 </expand>
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41 </inputs>
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42 <outputs>
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43 <data name="param_out" label="Output file" format="pepXML">
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44 <change_format>
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45 <when input="param_out_type" value="idXML" format="idXML"/>
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46 </change_format>
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47 </data>
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48 </outputs>
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49 <help>**What it does**
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50
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51 Converts identification engine file formats.
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52
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53
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54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html
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55
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56 @REFERENCES@
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57 </help>
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58 </tool>
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