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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDFileConverter" name="IDFileConverter" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_out_type:
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19 -out_type
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20 #if " " in str($param_out_type):
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21 "$param_out_type"
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22 #else
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23 $param_out_type
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24 #end if
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25 #end if
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26 #if $param_mz_file:
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27 -mz_file $param_mz_file
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28 #end if
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29 #if $param_mz_name:
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30 -mz_name "$param_mz_name"
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31 #end if
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32 #if $param_use_precursor_data:
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33 -use_precursor_data
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34 #end if
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35 #if $param_peptideprophet_analyzed:
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36 -peptideprophet_analyzed
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $adv_opts.adv_opts_selector=='advanced':
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40 #if $adv_opts.param_ignore_proteins_per_peptide:
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41 -ignore_proteins_per_peptide
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42 #end if
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43 #if $adv_opts.param_scan_regex:
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44 -scan_regex "$adv_opts.param_scan_regex"
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45 #end if
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #end if
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50 </command>
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51 <inputs>
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52 <param name="param_in" type="data" format="xml,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific XML format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml), <br>- for Sequest results, a directory containing .out files. <br>"/>
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53 <param name="param_out_type" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
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54 <option value="idXML">idXML</option>
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55 <option value="mzid">mzid</option>
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56 <option value="pepXML">pepXML</option>
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57 <option value="FASTA">FASTA</option>
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58 </param>
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59 <param name="param_mz_file" type="data" format="mzxml,mzml" optional="True" label="[Sequest, pepXML, mascotXML, XTandem only] Retention times will be looked up in this file" help="(-mz_file) "/>
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60 <param name="param_mz_name" type="text" size="30" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="(-mz_name) Only necessary if different from 'mz_file'">
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61 <sanitizer>
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62 <valid initial="string.printable">
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63 <remove value="'"/>
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64 <remove value="""/>
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65 </valid>
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66 </sanitizer>
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67 </param>
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68 <param name="param_use_precursor_data" type="boolean" truevalue="-use_precursor_data" falsevalue="" 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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69 <param name="param_peptideprophet_analyzed" type="boolean" truevalue="-peptideprophet_analyzed" falsevalue="" checked="false" optional="True" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results"/>
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70 <expand macro="advanced_options">
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71 <param name="param_ignore_proteins_per_peptide" type="boolean" truevalue="-ignore_proteins_per_peptide" falsevalue="" checked="false" optional="True" label="[Sequest only] Workaround to deal with .out files that contain" help="(-ignore_proteins_per_peptide) e.g. "+1" in references column, <br>but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
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72 <param name="param_scan_regex" type="text" size="30" label="[mascotXML only] Regular expression used to extract the scan number or retention time" help="(-scan_regex) See documentation for details">
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73 <sanitizer>
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74 <valid initial="string.printable">
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75 <remove value="'"/>
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76 <remove value="""/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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81 </expand>
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82 </inputs>
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83 <outputs>
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84 <data name="param_out" format="fasta"/>
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85 </outputs>
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86 <help>**What it does**
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87
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88 Converts identification engine file formats.
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89
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90
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91 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>
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92 <expand macro="references"/>
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93 </tool>
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