Mercurial > repos > galaxyp > openms_mztabexporter

annotate MzTabExporter.xml @ 13:2735db4dd8d9 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 19:23:13 +0000
parents 9bf4fbcf20c8
children 748dfbdf2201
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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: [File Handling]-->
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4 <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Exports various XML formats to an mzTab file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MzTabExporter</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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16 ## Preprocessing
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17 #if $in:
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18 mkdir in &&
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19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 #end if
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__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 #if $in:
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30 -in
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31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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32 #end if
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33 -out
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34 'out/output.${gxy2omsext("mztab")}'
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36 ## Postprocessing
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37 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
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46 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/>
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47 <param argument="-opt_columns" display="checkboxes" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help="">
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48 <option value="subfeatures" selected="true">subfeatures</option>
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49 <expand macro="list_string_san" name="opt_columns"/>
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50 </param>
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51 <expand macro="adv_opts_macro">
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52 <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/>
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53 <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/>
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54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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56 <expand macro="list_string_san" name="test"/>
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57 </param>
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58 </expand>
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59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
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65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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67 </data>
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68 </outputs>
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69 <tests><!-- TOPP_MzTabExporter_1 -->
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70 <test expect_num_outputs="2">
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71 <section name="adv_opts">
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72 <param name="first_run_inference_only" value="false"/>
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73 <param name="export_all_psms" value="false"/>
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74 <param name="force" value="false"/>
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75 <param name="test" value="true"/>
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76 </section>
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77 <param name="in" value="MzTabExporter_1_input.consensusXML"/>
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78 <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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79 <param name="opt_columns" value="subfeatures"/>
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80 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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81 <output name="ctd_out" ftype="xml">
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82 <assert_contents>
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83 <is_valid_xml/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 <!-- TOPP_MzTabExporter_2 -->
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88 <test expect_num_outputs="2">
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89 <section name="adv_opts">
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90 <param name="first_run_inference_only" value="false"/>
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91 <param name="export_all_psms" value="false"/>
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92 <param name="force" value="false"/>
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93 <param name="test" value="true"/>
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94 </section>
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95 <param name="in" value="MzTabExporter_2_input.idXML"/>
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96 <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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97 <param name="opt_columns" value="subfeatures"/>
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98 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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99 <output name="ctd_out" ftype="xml">
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100 <assert_contents>
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101 <is_valid_xml/>
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102 </assert_contents>
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103 </output>
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104 </test>
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105 <!-- TOPP_MzTabExporter_3 -->
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106 <test expect_num_outputs="2">
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107 <section name="adv_opts">
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108 <param name="first_run_inference_only" value="false"/>
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109 <param name="export_all_psms" value="false"/>
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110 <param name="force" value="false"/>
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111 <param name="test" value="true"/>
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112 </section>
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113 <param name="in" value="MzTabExporter_3_input.featureXML"/>
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114 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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115 <param name="opt_columns" value="subfeatures"/>
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116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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117 <output name="ctd_out" ftype="xml">
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118 <assert_contents>
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119 <is_valid_xml/>
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120 </assert_contents>
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121 </output>
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122 </test>
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123 <!-- TOPP_MzTabExporter_4 -->
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124 <test expect_num_outputs="2">
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125 <section name="adv_opts">
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126 <param name="first_run_inference_only" value="false"/>
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127 <param name="export_all_psms" value="false"/>
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128 <param name="force" value="false"/>
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129 <param name="test" value="true"/>
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130 </section>
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131 <param name="in" value="Epifany_2_out.consensusXML"/>
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132 <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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133 <param name="opt_columns" value="subfeatures"/>
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134 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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135 <output name="ctd_out" ftype="xml">
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136 <assert_contents>
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137 <is_valid_xml/>
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138 </assert_contents>
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139 </output>
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140 </test>
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141 <!-- TOPP_MzTabExporter_5 -->
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142 <test expect_num_outputs="2">
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143 <section name="adv_opts">
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144 <param name="first_run_inference_only" value="true"/>
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145 <param name="export_all_psms" value="false"/>
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146 <param name="force" value="false"/>
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147 <param name="test" value="true"/>
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148 </section>
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149 <param name="in" value="MzTabExporter_5_in.consensusXML"/>
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150 <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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151 <param name="opt_columns" value="subfeatures"/>
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152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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153 <output name="ctd_out" ftype="xml">
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154 <assert_contents>
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155 <is_valid_xml/>
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156 </assert_contents>
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157 </output>
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158 </test>
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159 <!-- TOPP_MzTabExporter_6 -->
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160 <test expect_num_outputs="2">
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161 <section name="adv_opts">
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162 <param name="first_run_inference_only" value="false"/>
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163 <param name="export_all_psms" value="false"/>
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164 <param name="force" value="false"/>
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165 <param name="test" value="true"/>
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166 </section>
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167 <param name="in" value="MzTabExporter_6_input.idXML"/>
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168 <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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169 <param name="opt_columns" value="subfeatures"/>
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170 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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171 <output name="ctd_out" ftype="xml">
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172 <assert_contents>
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173 <is_valid_xml/>
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174 </assert_contents>
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175 </output>
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176 </test>
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177 <!-- TOPP_MzTabExporter_7 -->
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178 <test expect_num_outputs="2">
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179 <section name="adv_opts">
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180 <param name="first_run_inference_only" value="false"/>
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181 <param name="export_all_psms" value="false"/>
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182 <param name="force" value="false"/>
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183 <param name="test" value="true"/>
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184 </section>
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185 <param name="in" value="MzTabExporter_7_input.consensusXML"/>
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186 <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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187 <param name="opt_columns" value="subfeatures"/>
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188 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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189 <output name="ctd_out" ftype="xml">
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190 <assert_contents>
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191 <is_valid_xml/>
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192 </assert_contents>
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193 </output>
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194 </test>
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195 <!-- TOPP_MzTabExporter_8 -->
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196 <test expect_num_outputs="2">
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197 <section name="adv_opts">
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198 <param name="first_run_inference_only" value="false"/>
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199 <param name="export_all_psms" value="true"/>
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200 <param name="force" value="false"/>
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201 <param name="test" value="true"/>
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202 </section>
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203 <param name="in" value="MzTabExporter_6_input.idXML"/>
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204 <output name="out" file="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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205 <param name="opt_columns" value="subfeatures"/>
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206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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207 <output name="ctd_out" ftype="xml">
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208 <assert_contents>
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209 <is_valid_xml/>
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210 </assert_contents>
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211 </output>
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212 </test>
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213 </tests>
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214 <help><![CDATA[Exports various XML formats to an mzTab file.
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215
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216
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217 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help>
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218 <expand macro="references"/>
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219 </tool>