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annotate IDFileConverter.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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="2.0.0">
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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>IDFileConverter
0
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_type:
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22 -out_type
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23 #if &quot; &quot; in str($param_out_type):
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24 &quot;$param_out_type&quot;
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25 #else
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26 $param_out_type
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27 #end if
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28 #end if
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29 #if $param_mz_file:
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30 -mz_file $param_mz_file
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31 #end if
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32 #if $param_mz_name:
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33 -mz_name &quot;$param_mz_name&quot;
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34 #end if
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35 #if $param_use_precursor_data:
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36 -use_precursor_data
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37 #end if
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38 #if $param_peptideprophet_analyzed:
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39 -peptideprophet_analyzed
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40 #end if
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41 #if $param_score_type:
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42 -score_type
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43 #if &quot; &quot; in str($param_score_type):
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44 &quot;$param_score_type&quot;
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45 #else
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46 $param_score_type
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47 #end if
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48 #end if
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49 -threads \${GALAXY_SLOTS:-24}
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50 #if $adv_opts.adv_opts_selector=='advanced':
4
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51 #if $adv_opts.param_ignore_proteins_per_peptide:
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52 -ignore_proteins_per_peptide
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53 #end if
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54 #if $adv_opts.param_scan_regex:
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55 -scan_regex &quot;$adv_opts.param_scan_regex&quot;
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56 #end if
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57 #if $adv_opts.param_count_from_zero:
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58 -count_from_zero
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59 #end if
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60 #if $adv_opts.param_force:
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61 -force
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62 #end if
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63 #end if
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64 </command>
4
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65 <inputs>
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66 <param format="tabular,xml,txt,pepxml" 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;" label="Input file or directory containing the data to convert" name="param_in" optional="False" type="data"/>
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67 <param help="(-out_type) " label="Output file type (default: determined from file extension)" name="param_out_type" optional="True" type="select">
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68 <option value="idXML">idXML</option>
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69 <option value="mzid">mzid</option>
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70 <option value="pepXML">pepXML</option>
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71 <option value="FASTA">FASTA</option>
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72 </param>
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73 <param format="xml,mzxml,mzml" help="(-mz_file) " label="[pepXML, Sequest, Mascot, X! Tandem, Percolator only] Retention times will be looked up in this file" name="param_mz_file" optional="True" type="data"/>
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74 <param help="(-mz_name) Only necessary if different from 'mz_file'" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" name="param_mz_name" size="30" type="text">
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75 <sanitizer>
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76 <valid initial="string.printable">
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77 <remove value="'"/>
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78 <remove value="&quot;"/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 <param checked="false" falsevalue="" help="(-use_precursor_data) " 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" name="param_use_precursor_data" optional="True" truevalue="-use_precursor_data" type="boolean"/>
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83 <param checked="false" falsevalue="" help="(-peptideprophet_analyzed) By default a 'raw' pepXML is produced that contains only search engine results" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" name="param_peptideprophet_analyzed" optional="True" truevalue="-peptideprophet_analyzed" type="boolean"/>
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84 <param help="(-score_type) " label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" name="param_score_type" optional="True" type="select" value="qvalue">
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85 <option value="qvalue">qvalue</option>
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86 <option value="PEP">PEP</option>
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87 <option value="score">score</option>
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88 </param>
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89 <expand macro="advanced_options">
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90 <param checked="false" falsevalue="" 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)" label="[Sequest only] Workaround to deal with .out files that contain" name="param_ignore_proteins_per_peptide" optional="True" truevalue="-ignore_proteins_per_peptide" type="boolean"/>
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91 <param help="(-scan_regex) See documentation for details" label="[Mascot, Percolator only] Regular expression used to extract the scan number or retention time" name="param_scan_regex" size="30" type="text">
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92 <sanitizer>
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93 <valid initial="string.printable">
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94 <remove value="'"/>
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95 <remove value="&quot;"/>
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96 </valid>
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97 </sanitizer>
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98 </param>
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99 <param checked="false" falsevalue="" help="(-count_from_zero) " label="[Percolator only] Scan numbers extracted by 'scan_regex' start counting at zero (default: start at one)" name="param_count_from_zero" optional="True" truevalue="-count_from_zero" type="boolean"/>
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100 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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101 </expand>
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102 </inputs>
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103 <outputs>
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104 <data format="xml" name="param_out"/>
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105 </outputs>
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106 <help>Converts identification engine file formats.
0
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107
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108
4
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109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>
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110 </tool>