Mercurial > repos > galaxyp > openms_proteinresolver

annotate ProteinResolver.xml @ 13:851f7c252d66 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:57:06 +0000
parents 95f90fab5ce8
children c2612cb89529
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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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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@VERSION_SUFFIX@" profile="21.05">
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5 <description>protein inference</description>
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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 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 mkdir fasta &&
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18 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
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19 #if $in_cond.in:
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20 mkdir in_cond.in &&
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21 #if $in_cond.in_select == "no"
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22 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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23 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
851f7c252d66 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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24 #else
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25 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
851f7c252d66 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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26 #end if
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27 #end if
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28 #if $design:
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29 mkdir design &&
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30 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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31 #end if
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32 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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33 mkdir protein_groups &&
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34 #end if
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35 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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36 mkdir peptide_table &&
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37 #end if
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38 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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39 mkdir protein_table &&
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40 #end if
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41 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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42 mkdir additional_info &&
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43 #end if
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44
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45 ## Main program call
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46
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47 set -o pipefail &&
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48 @EXECUTABLE@ -write_ctd ./ &&
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49 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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50 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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51 -fasta
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52 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
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53 #if $in_cond.in:
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54 -in
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55 #if $in_cond.in_select == "no"
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56 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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57 #else
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58 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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59 #end if
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60 #end if
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61 #if $design:
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62 -design
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63 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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64 #end if
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65 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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66 -protein_groups
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67 'protein_groups/output.${gxy2omsext("csv")}'
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68 #end if
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69 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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70 -peptide_table
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71 'peptide_table/output.${gxy2omsext("csv")}'
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72 #end if
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73 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 -protein_table
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75 'protein_table/output.${gxy2omsext("csv")}'
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76 #end if
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77 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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78 -additional_info
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79 'additional_info/output.${gxy2omsext("csv")}'
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80 #end if
9
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81 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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82 | tee '$stdout'
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83 #end if
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84
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85 ## Postprocessing
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86 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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87 && mv 'protein_groups/output.${gxy2omsext("csv")}' '$protein_groups'
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88 #end if
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89 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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90 && mv 'peptide_table/output.${gxy2omsext("csv")}' '$peptide_table'
0
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91 #end if
9
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92 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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93 && mv 'protein_table/output.${gxy2omsext("csv")}' '$protein_table'
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94 #end if
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95 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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96 && mv 'additional_info/output.${gxy2omsext("csv")}' '$additional_info'
0
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97 #end if
9
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98 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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99 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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100 #end if]]></command>
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101 <configfiles>
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102 <inputs name="args_json" data_style="paths"/>
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103 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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104 </configfiles>
0
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105 <inputs>
13
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106 <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/>
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107 <conditional name="in_cond">
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108 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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109 <option value="no">No: process all datasets jointly</option>
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110 <option value="yes">Yes: process each dataset in an independent job</option>
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111 </param>
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112 <when value="no">
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113 <param 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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114 </when>
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115 <when value="yes">
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116 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
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117 </when>
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118 </conditional>
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119 <param 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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120 <expand macro="list_string_san" name="in_path"/>
0
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121 </param>
13
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122 <param 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)"/>
9
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123 <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
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124 <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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125 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/>
13
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126 <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help="">
9
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127 <option value="Trypsin" selected="true">Trypsin</option>
13
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128 <expand macro="list_string_san" name="enzyme"/>
9
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129 </param>
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130 </section>
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131 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
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132 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
13
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133 <expand macro="list_string_san" name="experiment"/>
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134 </param>
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135 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help="">
13
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136 <expand macro="list_string_san" name="file"/>
9
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137 </param>
13
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138 <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help="">
9
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139 <option value="tab" selected="true">tab</option>
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140 <option value="semi-colon">semi-colon</option>
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141 <option value="comma">comma</option>
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142 <option value="whitespace">whitespace</option>
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143 <expand macro="list_string_san" name="separator"/>
9
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144 </param>
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145 </section>
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146 <expand macro="adv_opts_macro">
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147 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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148 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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149 <expand macro="list_string_san" name="test"/>
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150 </param>
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151 </expand>
11
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152 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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153 <option value="protein_groups_FLAG">protein_groups (output file. Contains all protein groups)</option>
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154 <option value="peptide_table_FLAG">peptide_table (output file)</option>
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155 <option value="protein_table_FLAG">protein_table (output file. Contains one protein per line)</option>
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156 <option value="additional_info_FLAG">additional_info (output file for additional info)</option>
9
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157 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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158 </param>
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159 </inputs>
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160 <outputs>
9
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161 <data name="protein_groups" label="${tool.name} on ${on_string}: protein_groups" format="csv">
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162 <filter>OPTIONAL_OUTPUTS is not None and "protein_groups_FLAG" in OPTIONAL_OUTPUTS</filter>
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163 </data>
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164 <data name="peptide_table" label="${tool.name} on ${on_string}: peptide_table" format="csv">
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165 <filter>OPTIONAL_OUTPUTS is not None and "peptide_table_FLAG" in OPTIONAL_OUTPUTS</filter>
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166 </data>
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167 <data name="protein_table" label="${tool.name} on ${on_string}: protein_table" format="csv">
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168 <filter>OPTIONAL_OUTPUTS is not None and "protein_table_FLAG" in OPTIONAL_OUTPUTS</filter>
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169 </data>
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170 <data name="additional_info" label="${tool.name} on ${on_string}: additional_info" format="csv">
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171 <filter>OPTIONAL_OUTPUTS is not None and "additional_info_FLAG" in OPTIONAL_OUTPUTS</filter>
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172 </data>
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173 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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174 <filter>OPTIONAL_OUTPUTS is None</filter>
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175 </data>
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176 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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177 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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178 </data>
0
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179 </outputs>
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180 <tests><!-- TOPP_ProteinResolver_1 -->
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181 <test expect_num_outputs="4">
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182 <section name="adv_opts">
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183 <param name="force" value="false"/>
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184 <param name="test" value="true"/>
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185 </section>
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186 <param name="fasta" value="ProteinResolver_1_input.fasta"/>
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187 <conditional name="in_cond">
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188 <param name="in" value="ProteinResolver_1_input.consensusXML"/>
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189 </conditional>
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190 <param name="in_path" value=""/>
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191 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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192 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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193 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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194 <section name="resolver">
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195 <param name="missed_cleavages" value="2"/>
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196 <param name="min_length" value="6"/>
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197 <param name="enzyme" value="Trypsin"/>
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198 </section>
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199 <section name="designer">
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200 <param name="experiment" value="ExperimentalSetting"/>
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201 <param name="file" value="File"/>
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202 <param name="separator" value="tab"/>
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203 </section>
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204 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/>
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205 <output name="ctd_out" ftype="xml">
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206 <assert_contents>
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207 <is_valid_xml/>
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208 </assert_contents>
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209 </output>
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210 </test>
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211 </tests>
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212 <help><![CDATA[protein inference
0
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213
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214
13
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215 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help>
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216 <expand macro="references"/>
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217 </tool>