Mercurial > repos > galaxyp > openms_idfileconverter

annotate IDFileConverter.xml @ 11:43a1db77b7a6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:55:15 +0000
parents 83cf7a4cd03c
children 250d6a43f66b
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="IDFileConverter" name="IDFileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if $mz_file:
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23 mkdir mz_file &&
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24 ln -s '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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35 -out
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36 'out/output.${out_type}'
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37 #if $mz_file:
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38 -mz_file
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39 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)'
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40 #end if
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42 ## Postprocessing
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43 && mv 'out/output.${out_type}' '$out'
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44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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46 #end if]]></command>
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47 <configfiles>
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48 <inputs name="args_json" data_style="paths"/>
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49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="in" argument="-in" type="data" format="idxml,mascotxml,mzid,pepxml,protxml,psms,tabular,xml,xquest.xml" optional="false" label="Input file or directory containing the data to convert" help="This may be:. - a single file in a multi-purpose XML format (.pepXML, .protXML, .idXML, .mzid),. - a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),. - a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),. - for Sequest results, a directory containing .out files.. select idxml,mascotxml,mzid,pepxml,protxml,psms,tabular,xml,xquest.xml data sets(s)"/>
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53 <param name="out_type" argument="-out_type" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
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54 <option value="FASTA">fasta</option>
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55 <option value="idXML">idxml</option>
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56 <option value="mzid">mzid</option>
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57 <option value="pepXML">pepxml</option>
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58 <option value="xquest.xml">xquest.xml</option>
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59 <expand macro="list_string_san"/>
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60 </param>
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61 <param name="mz_file" argument="-mz_file" type="data" format="mzdata,mzml,mzxml" optional="true" label="[pepXML, Sequest, Mascot, X" help="Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file select mzdata,mzml,mzxml data sets(s)"/>
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62 <param name="mz_name" argument="-mz_name" type="text" optional="true" value="" label="[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute)" help="Only necessary if different from 'mz_file'">
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63 <expand macro="list_string_san"/>
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64 </param>
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65 <param name="peptideprophet_analyzed" argument="-peptideprophet_analyzed" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[pepXML output only] Write output in the format of a PeptideProphet analysis result" help="By default a 'raw' pepXML is produced that contains only search engine results"/>
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66 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit" help="">
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67 <option value="qvalue" selected="true">qvalue</option>
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68 <option value="PEP">PEP</option>
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69 <option value="score">score</option>
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70 <expand macro="list_string_san"/>
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71 </param>
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72 <expand macro="adv_opts_macro">
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73 <param name="ignore_proteins_per_peptide" argument="-ignore_proteins_per_peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[Sequest only] Workaround to deal with .out files that contain" help="e.g. &quot;+1&quot; in references column,. but do not list extra references in subsequent lines (try -debug 3 or 4)"/>
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74 <param name="scan_regex" argument="-scan_regex" type="text" optional="true" value="" label="[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time" help="See documentation for details">
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75 <expand macro="list_string_san"/>
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76 </param>
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77 <param name="no_spectra_data_override" argument="-no_spectra_data_override" type="boolean" truevalue="true" falsevalue="false" checked="false" 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="Use only if you are sure it is absolutely the same mz_file as used for identification"/>
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78 <param name="no_spectra_references_override" argument="-no_spectra_references_override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[+mz_file only] Setting this flag will avoid overriding 'spectrum_reference' in PeptideIdentifications if mz_file is given and a 'spectrum_reference' is already present" help=""/>
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79 <param name="add_ionmatch_annotation" argument="-add_ionmatch_annotation" type="float" optional="true" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="Will take quite some while. Match tolerance is .4"/>
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80 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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81 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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82 <expand macro="list_string_san"/>
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83 </param>
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84 </expand>
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85 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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87 </param>
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88 </inputs>
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89 <outputs>
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90 <data name="out" label="${tool.name} on ${on_string}: out">
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91 <change_format>
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92 <when input="out_type" value="FASTA" format="fasta"/>
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93 <when input="out_type" value="idXML" format="idxml"/>
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94 <when input="out_type" value="mzid" format="mzid"/>
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95 <when input="out_type" value="pepXML" format="pepxml"/>
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96 <when input="out_type" value="xquest.xml" format="xquest.xml"/>
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97 </change_format>
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98 </data>
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99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <expand macro="autotest_IDFileConverter"/>
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105 <expand macro="manutest_IDFileConverter"/>
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106 </tests>
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107 <help><![CDATA[Converts identification engine file formats.
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108
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109
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110 For more information, visit http://www.openms.de/documentation/TOPP_IDFileConverter.html]]></help>
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111 <expand macro="references"/>
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112 </tool>