Mercurial > repos > galaxyp > openms_qccalculator

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:34:05 +0000
parents d0607dfea8fa
children
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988cd0f185ee planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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2 <!--Proposed Tool Section: []-->
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3 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">QCCalculator</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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19 #if $id:
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20 mkdir id &&
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21 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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22 #end if
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23 #if $feature:
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24 mkdir feature &&
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25 cp '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
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26 #end if
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27 #if $consensus:
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28 mkdir consensus &&
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29 cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
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30 #end if
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32 ## Main program call
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 -in
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39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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40 -out
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41 'out/output.${out_type}'
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42 #if $id:
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43 -id
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44 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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45 #end if
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46 #if $feature:
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47 -feature
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48 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)'
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49 #end if
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50 #if $consensus:
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51 -consensus
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52 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)'
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53 #end if
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55 ## Postprocessing
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56 && mv 'out/output.${out_type}' '$out'
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57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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58 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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59 #end if]]></command>
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60 <configfiles>
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61 <inputs name="args_json" data_style="paths"/>
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62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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63 </configfiles>
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64 <inputs>
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65 <param argument="-in" type="data" format="mzml" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
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66 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
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67 <option value="mzQC">mzqc</option>
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68 <option value="qcML">qcml</option>
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69 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
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70 <expand macro="list_string_san" name="out_type"/>
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71 </param>
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72 <param argument="-label" type="text" value="label" label="unique name for the run that can be used in a figure label" help="">
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73 <expand macro="list_string_san" name="label"/>
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74 </param>
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75 <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help="">
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76 <expand macro="list_string_san" name="name"/>
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77 </param>
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78 <param argument="-address" type="text" optional="true" value="" label="contact address (mail/e-mail or phone)" help="">
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79 <expand macro="list_string_san" name="address"/>
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80 </param>
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81 <param argument="-description" type="text" optional="true" value="" label="description and comments about the mzQC file contents" help="">
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82 <expand macro="list_string_san" name="description"/>
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83 </param>
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84 <param argument="-id" type="data" format="idxml" optional="true" label="Input idXML file containing the identifications" help="Your identifications will be exported in an easy-to-read format select idxml data sets(s)"/>
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85 <param argument="-feature" type="data" format="featurexml" optional="true" label="feature input file (this is relevant for most QC issues)" help=" select featurexml data sets(s)"/>
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86 <param argument="-consensus" type="data" format="consensusxml" optional="true" label="consensus input file (this is only used for charge state deconvoluted output" help="Use the consensusXML output form the DeCharger) select consensusxml data sets(s)"/>
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87 <param argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/>
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88 <expand macro="adv_opts_macro">
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89 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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90 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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91 <expand macro="list_string_san" name="test"/>
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92 </param>
0
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93 </expand>
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94 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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96 </param>
0
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97 </inputs>
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98 <outputs>
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99 <data name="out" label="${tool.name} on ${on_string}: out" format="mzqc">
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100 <change_format>
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101 <when input="out_type" value="qcML" format="qcml"/>
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102 </change_format>
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103 </data>
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104 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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105 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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106 </data>
0
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107 </outputs>
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108 <tests>
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109 <!-- TOPP_QCCalculator_1 -->
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110 <test expect_num_outputs="2">
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111 <section name="adv_opts">
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112 <param name="force" value="false"/>
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113 <param name="test" value="true"/>
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114 </section>
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115 <param name="in" value="QCCalculator_input.mzML"/>
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116 <output name="out" value="QCCalculator_1_output.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
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117 <param name="out_type" value="qcML"/>
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118 <param name="label" value="label"/>
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119 <param name="name" value=""/>
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120 <param name="address" value=""/>
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121 <param name="description" value=""/>
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122 <param name="remove_duplicate_features" value="false"/>
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123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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124 <output name="ctd_out" ftype="xml">
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125 <assert_contents>
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126 <is_valid_xml/>
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127 </assert_contents>
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128 </output>
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129 <assert_stdout>
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130 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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131 </assert_stdout>
13
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132 </test>
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133 <!-- TOPP_QCCalculator_2 -->
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134 <test expect_num_outputs="2">
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135 <section name="adv_opts">
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136 <param name="force" value="false"/>
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137 <param name="test" value="true"/>
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138 </section>
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139 <param name="in" value="QCCalculator_input.mzML"/>
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140 <output name="out" value="QCCalculator_2_output.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
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141 <param name="out_type" value="mzQC"/>
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142 <param name="label" value="label"/>
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143 <param name="name" value="name"/>
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144 <param name="address" value="address"/>
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145 <param name="description" value="description"/>
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146 <param name="id" value="OpenPepXL_output.idXML"/>
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147 <param name="feature" value="FeatureFinderMetaboIdent_1_output.featureXML"/>
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148 <param name="remove_duplicate_features" value="false"/>
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149 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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150 <output name="ctd_out" ftype="xml">
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151 <assert_contents>
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152 <is_valid_xml/>
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153 </assert_contents>
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154 </output>
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155 <assert_stdout>
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156 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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157 </assert_stdout>
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158 </test>
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159 <test expect_num_outputs="1">
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160 <!-- took test data from another test w mzML input -->
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161 <param name="adv_opts|test" value="true"/>
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162 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
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163 <param name="out_type" value="qcML"/>
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164 <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
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165 </test>
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166 <test expect_num_outputs="1">
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167 <!-- took test data from another test w mzML,idXML,consensusXML input -->
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168 <param name="adv_opts|test" value="true"/>
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169 <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
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170 <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
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171 <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
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172 <param name="out_type" value="qcML"/>
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173 <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
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174 </test>
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175 <test expect_num_outputs="1">
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176 <!-- took test data from another test w mzML,idXML,featureXML input -->
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177 <param name="adv_opts|test" value="true"/>
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178 <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
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179 <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
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180 <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
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181 <param name="out_type" value="qcML"/>
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182 <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
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183 </test>
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184 </tests>
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185 <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
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186
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187
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188 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCCalculator.html]]></help>
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189 <expand macro="references"/>
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190 </tool>