Mercurial > repos > galaxyp > openms_digestor

annotate Digestor.xml @ 10:7af5860ae563 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:23:17 +0000
parents 688f329e6583
children 4827e132ac53
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e661b6359f66 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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Digests a protein database in-silico.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Digestor</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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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($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${out_type}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${out_type}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
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45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
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46 <option value="fasta">fasta</option>
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47 <option value="idXML">idxml</option>
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48 <expand macro="list_string_san"/>
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49 </param>
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50 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
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51 <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
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52 <param name="max_length" argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
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53 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The type of digestion enzyme" help="">
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54 <option value="Asp-N">Asp-N</option>
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55 <option value="Asp-N/B">Asp-N/B</option>
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56 <option value="Asp-N_ambic">Asp-N_ambic</option>
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57 <option value="cyanogen-bromide">cyanogen-bromide</option>
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58 <option value="Clostripain/P">Clostripain/P</option>
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59 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
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60 <option value="no cleavage">no cleavage</option>
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61 <option value="unspecific cleavage">unspecific cleavage</option>
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62 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
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63 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
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64 <option value="Glu-C+P">Glu-C+P</option>
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65 <option value="PepsinA + P">PepsinA + P</option>
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66 <option value="leukocyte elastase">leukocyte elastase</option>
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67 <option value="proline endopeptidase">proline endopeptidase</option>
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68 <option value="Chymotrypsin">Chymotrypsin</option>
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69 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
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70 <option value="CNBr">CNBr</option>
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71 <option value="Formic_acid">Formic_acid</option>
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72 <option value="Lys-C">Lys-C</option>
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73 <option value="Lys-N">Lys-N</option>
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74 <option value="Lys-C/P">Lys-C/P</option>
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75 <option value="PepsinA">PepsinA</option>
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76 <option value="TrypChymo">TrypChymo</option>
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77 <option value="Trypsin/P">Trypsin/P</option>
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78 <option value="V8-DE">V8-DE</option>
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79 <option value="V8-E">V8-E</option>
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80 <option value="Arg-C">Arg-C</option>
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81 <option value="Arg-C/P">Arg-C/P</option>
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82 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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83 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
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84 <option value="2-iodobenzoate">2-iodobenzoate</option>
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85 <option value="iodosobenzoate">iodosobenzoate</option>
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86 <option value="Trypsin" selected="true">Trypsin</option>
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87 <expand macro="list_string_san"/>
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88 </param>
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89 <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
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90 <param name="ID" argument="-FASTA:ID" display="radio" type="select" optional="false" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
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91 <option value="parent" selected="true">parent</option>
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92 <option value="number">number</option>
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93 <option value="both">both</option>
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94 <expand macro="list_string_san"/>
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95 </param>
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96 <param name="description" argument="-FASTA:description" display="radio" type="select" optional="false" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
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97 <option value="remove" selected="true">remove</option>
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98 <option value="keep">keep</option>
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99 <expand macro="list_string_san"/>
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100 </param>
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101 </section>
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102 <expand macro="adv_opts_macro">
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103 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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104 <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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105 <expand macro="list_string_san"/>
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106 </param>
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107 </expand>
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108 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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110 </param>
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111 </inputs>
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112 <outputs>
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113 <data name="out" label="${tool.name} on ${on_string}: out">
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114 <change_format>
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115 <when input="out_type" value="fasta" format="fasta"/>
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116 <when input="out_type" value="idXML" format="idxml"/>
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117 </change_format>
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118 </data>
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119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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121 </data>
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122 </outputs>
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123 <tests>
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124 <expand macro="autotest_Digestor"/>
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125 <expand macro="manutest_Digestor"/>
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126 </tests>
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127 <help><![CDATA[Digests a protein database in-silico.
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128
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129
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130 For more information, visit http://www.openms.de/documentation/UTILS_Digestor.html]]></help>
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131 <expand macro="references"/>
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132 </tool>