Mercurial > repos > galaxyp > openms_idfileconverter

annotate IDFileConverter.xml @ 4:4b4582790bbd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:17:45 -0400
parents 066cf4d993f5
children 1dcffdad49c0
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bea4646ed591 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="IDFileConverter" name="IDFileConverter" version="2.2.0">
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5 <description>Converts identification engine file formats.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDFileConverter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command><![CDATA[
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15 ## check input file type
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16 #set $in_type = $param_in.ext
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17
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18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
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19 ln -s '$param_in' 'param_in.${in_type}' &&
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21 IDFileConverter
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22
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23 #if $param_in:
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24 -in 'param_in.${in_type}'
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25 #end if
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26 #if $param_out:
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27 -out $param_out
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28 #end if
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29 #if $param_out_type:
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30 -out_type
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31 #if " " in str($param_out_type):
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32 "$param_out_type"
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33 #else
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34 $param_out_type
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35 #end if
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36 #end if
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37 #if $param_mz_file:
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38 -mz_file $param_mz_file
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39 #end if
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40 #if $param_mz_name:
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41 -mz_name "$param_mz_name"
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42 #end if
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43 #if $param_peptideprophet_analyzed:
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44 -peptideprophet_analyzed
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45 #end if
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46 #if $param_score_type:
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47 -score_type
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48 #if " " in str($param_score_type):
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49 "$param_score_type"
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50 #else
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51 $param_score_type
1
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52 #end if
3
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53 #end if
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54 #if $adv_opts.adv_opts_selector=='advanced':
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55 #if $adv_opts.param_ignore_proteins_per_peptide:
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56 -ignore_proteins_per_peptide
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57 #end if
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58 #if $adv_opts.param_scan_regex:
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59 -scan_regex "$adv_opts.param_scan_regex"
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60 #end if
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61 #if $adv_opts.param_no_spectra_data_override:
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62 -no_spectra_data_override
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63 #end if
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64 #if $adv_opts.param_force:
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65 -force
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66 #end if
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67 #end if
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68 ]]>
0
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69 </command>
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70 <inputs>
3
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71 <param name="param_in" type="data" format="pepxml,protXML,mascotXML,omssaXML,xml,psms,tabular,idxml,mzid" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
0
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72 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
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73 <option value="idXML">idXML</option>
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74 <option value="mzid">mzid</option>
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75 <option value="pepXML">pepXML</option>
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76 <option value="FASTA">FASTA</option>
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77 </param>
3
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78 <param name="param_mz_file" type="data" format="mzml,mzxml,mzData" optional="True" label="[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file" help="(-mz_file) "/>
0
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79 <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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80 <sanitizer>
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81 <valid initial="string.printable">
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82 <remove value="'"/>
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83 <remove value="&quot;"/>
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84 </valid>
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85 </sanitizer>
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86 </param>
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87 <param name="param_peptideprophet_analyzed" display="radio" 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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88 <param name="param_score_type" display="radio" type="select" optional="False" value="qvalue" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="(-score_type) ">
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89 <option value="qvalue" selected="true">qvalue</option>
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90 <option value="PEP">PEP</option>
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91 <option value="score">score</option>
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92 </param>
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93 <expand macro="advanced_options">
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94 <param name="param_ignore_proteins_per_peptide" display="radio" 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. &quot;+1&quot; in references column, &lt;br&gt;but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
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95 <param name="param_scan_regex" type="text" size="30" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="(-scan_regex) See documentation for details">
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96 <sanitizer>
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97 <valid initial="string.printable">
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98 <remove value="'"/>
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99 <remove value="&quot;"/>
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100 </valid>
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101 </sanitizer>
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102 </param>
3
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103 <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
0
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104 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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105 </expand>
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106 </inputs>
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107 <outputs>
2
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108 <data name="param_out" auto_format="true"/>
0
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109 </outputs>
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110 <help>Converts identification engine file formats.
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111
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112
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113 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>
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114 </tool>