Mercurial > repos > galaxyp > openms_proteinresolver

annotate ProteinResolver.xml @ 10:f7ef238cc21e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:10:44 +0000
parents 814d6f4706e3
children 95f90fab5ce8
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154998956e7a 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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dc9abec0379f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Quantitation]-->
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4 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>protein inference</description>
154998956e7a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinResolver</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>
154998956e7a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir fasta &&
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20 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
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21 #if $in:
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22 mkdir in &&
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23 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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154998956e7a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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24 #end if
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25 #if $design:
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26 mkdir design &&
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27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 #end if
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29 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 mkdir protein_groups &&
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154998956e7a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 #end if
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32 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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33 mkdir peptide_table &&
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34 #end if
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35 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 mkdir protein_table &&
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154998956e7a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 #end if
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38 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 mkdir additional_info &&
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40 #end if
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814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 ## Main program call
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814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 set -o pipefail &&
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45 @EXECUTABLE@ -write_ctd ./ &&
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46 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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47 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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48 -fasta
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49 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
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50 #if $in:
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51 -in
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52 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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53 #end if
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54 #if $design:
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55 -design
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56 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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57 #end if
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58 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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59 -protein_groups
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60 'protein_groups/output.${gxy2omsext("csv")}'
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61 #end if
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62 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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63 -peptide_table
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64 'peptide_table/output.${gxy2omsext("csv")}'
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65 #end if
9
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66 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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67 -protein_table
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68 'protein_table/output.${gxy2omsext("csv")}'
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69 #end if
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70 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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71 -additional_info
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72 'additional_info/output.${gxy2omsext("csv")}'
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73 #end if
9
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74 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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75 | tee '$stdout'
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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76 #end if
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77
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78 ## Postprocessing
814d6f4706e3 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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79 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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80 && mv 'protein_groups/output.${gxy2omsext("csv")}' '$protein_groups'
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81 #end if
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82 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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83 && mv 'peptide_table/output.${gxy2omsext("csv")}' '$peptide_table'
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84 #end if
9
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85 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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86 && mv 'protein_table/output.${gxy2omsext("csv")}' '$protein_table'
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87 #end if
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88 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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89 && mv 'additional_info/output.${gxy2omsext("csv")}' '$additional_info'
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90 #end if
9
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91 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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92 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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93 #end if]]></command>
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94 <configfiles>
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95 <inputs name="args_json" data_style="paths"/>
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96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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97 </configfiles>
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98 <inputs>
9
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99 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/>
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100 <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
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101 <param name="in_path" argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given">
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102 <expand macro="list_string_san"/>
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103 </param>
9
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104 <param name="design" argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/>
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105 <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
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106 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
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107 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/>
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108 <param name="enzyme" argument="-resolver:enzyme" display="radio" type="select" optional="false" label="Digestion enzyme" help="">
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109 <option value="Trypsin" selected="true">Trypsin</option>
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110 <expand macro="list_string_san"/>
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111 </param>
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112 </section>
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113 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
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114 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
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115 <expand macro="list_string_san"/>
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116 </param>
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117 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help="">
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118 <expand macro="list_string_san"/>
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119 </param>
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120 <param name="separator" argument="-designer:separator" display="radio" type="select" optional="false" label="Separator, which should be used to split a row into columns" help="">
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121 <option value="tab" selected="true">tab</option>
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122 <option value="semi-colon">semi-colon</option>
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123 <option value="comma">comma</option>
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124 <option value="whitespace">whitespace</option>
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125 <expand macro="list_string_san"/>
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126 </param>
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127 </section>
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128 <expand macro="adv_opts_macro">
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129 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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130 <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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131 <expand macro="list_string_san"/>
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132 </param>
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133 </expand>
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134 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
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135 <option value="protein_groups_FLAG">protein_groups (Separator, which should be used to split a row into columns)</option>
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136 <option value="peptide_table_FLAG">peptide_table (Separator, which should be used to split a row into columns)</option>
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137 <option value="protein_table_FLAG">protein_table (Separator, which should be used to split a row into columns)</option>
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138 <option value="additional_info_FLAG">additional_info (Separator, which should be used to split a row into columns)</option>
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139 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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140 </param>
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141 </inputs>
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142 <outputs>
9
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143 <data name="protein_groups" label="${tool.name} on ${on_string}: protein_groups" format="csv">
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144 <filter>OPTIONAL_OUTPUTS is not None and "protein_groups_FLAG" in OPTIONAL_OUTPUTS</filter>
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145 </data>
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146 <data name="peptide_table" label="${tool.name} on ${on_string}: peptide_table" format="csv">
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147 <filter>OPTIONAL_OUTPUTS is not None and "peptide_table_FLAG" in OPTIONAL_OUTPUTS</filter>
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148 </data>
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149 <data name="protein_table" label="${tool.name} on ${on_string}: protein_table" format="csv">
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150 <filter>OPTIONAL_OUTPUTS is not None and "protein_table_FLAG" in OPTIONAL_OUTPUTS</filter>
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151 </data>
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152 <data name="additional_info" label="${tool.name} on ${on_string}: additional_info" format="csv">
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153 <filter>OPTIONAL_OUTPUTS is not None and "additional_info_FLAG" in OPTIONAL_OUTPUTS</filter>
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154 </data>
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155 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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156 <filter>OPTIONAL_OUTPUTS is None</filter>
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157 </data>
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158 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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159 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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160 </data>
0
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161 </outputs>
9
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162 <tests>
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163 <expand macro="autotest_ProteinResolver"/>
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164 <expand macro="manutest_ProteinResolver"/>
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165 </tests>
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166 <help><![CDATA[protein inference
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168
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169 For more information, visit http://www.openms.de/documentation/TOPP_ProteinResolver.html]]></help>
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170 <expand macro="references"/>
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171 </tool>