Mercurial > repos > galaxyp > openms_ticcalculator

annotate TICCalculator.xml @ 14:5f36444a0f9d draft default tip

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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 21:43:12 +0000
parents d623ad21ca59
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11fc1eb69276 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="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">TICCalculator</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($in.ext)' &&
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19 ## Main program call
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21 set -o pipefail &&
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22 @EXECUTABLE@ -write_ctd ./ &&
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23 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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24 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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25 -in
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26 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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27 | tee '$stdout'
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29 ## Postprocessing
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30 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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31 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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32 #end if]]></command>
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33 <configfiles>
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34 <inputs name="args_json" data_style="paths"/>
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35 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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36 </configfiles>
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37 <inputs>
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38 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
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39 <param argument="-read_method" type="select" label="Method to read the file" help="">
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40 <option value="regular" selected="true">regular</option>
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41 <option value="indexed">indexed</option>
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42 <option value="indexed_parallel">indexed_parallel</option>
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43 <option value="streaming">streaming</option>
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44 <option value="cached">cached</option>
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45 <option value="cached_parallel">cached_parallel</option>
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46 <expand macro="list_string_san" name="read_method"/>
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47 </param>
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48 <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/>
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49 <expand macro="adv_opts_macro">
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50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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51 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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52 <expand macro="list_string_san" name="test"/>
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53 </param>
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54 </expand>
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55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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61 <filter>OPTIONAL_OUTPUTS is None</filter>
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62 </data>
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63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <!-- TOPP_TICCalculator_1 -->
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69 <test expect_num_outputs="1">
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70 <section name="adv_opts">
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71 <param name="force" value="false"/>
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72 <param name="test" value="true"/>
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73 </section>
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74 <param name="in" value="MapNormalizer_output.mzML"/>
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75 <param name="read_method" value="regular"/>
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76 <param name="loadData" value="true"/>
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77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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78 <output name="ctd_out" ftype="xml">
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79 <assert_contents>
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80 <is_valid_xml/>
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81 </assert_contents>
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82 </output>
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83 <assert_stdout>
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84 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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85 </assert_stdout>
13
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86 </test>
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87 <!-- TOPP_TICCalculator_2 -->
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88 <test expect_num_outputs="1">
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89 <section name="adv_opts">
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90 <param name="force" value="false"/>
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91 <param name="test" value="true"/>
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92 </section>
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93 <param name="in" value="MapNormalizer_output.mzML"/>
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94 <param name="read_method" value="streaming"/>
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95 <param name="loadData" value="true"/>
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96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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97 <output name="ctd_out" ftype="xml">
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98 <assert_contents>
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99 <is_valid_xml/>
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100 </assert_contents>
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101 </output>
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102 <assert_stdout>
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103 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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104 </assert_stdout>
13
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105 </test>
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106 <!-- TOPP_TICCalculator_3 -->
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107 <test expect_num_outputs="1">
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108 <section name="adv_opts">
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109 <param name="force" value="false"/>
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110 <param name="test" value="true"/>
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111 </section>
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112 <param name="in" value="MapNormalizer_output.mzML"/>
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113 <param name="read_method" value="streaming"/>
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114 <param name="loadData" value="false"/>
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115 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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116 <output name="ctd_out" ftype="xml">
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117 <assert_contents>
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118 <is_valid_xml/>
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119 </assert_contents>
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120 </output>
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121 <assert_stdout>
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122 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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123 </assert_stdout>
13
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124 </test>
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125 <!-- TOPP_TICCalculator_4 -->
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126 <test expect_num_outputs="1">
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127 <section name="adv_opts">
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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="MapNormalizer_output.mzML"/>
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132 <param name="read_method" value="indexed"/>
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133 <param name="loadData" value="true"/>
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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>
14
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140 <assert_stdout>
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141 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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142 </assert_stdout>
13
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143 </test>
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144 <!-- TOPP_TICCalculator_5 -->
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145 <test expect_num_outputs="1">
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146 <section name="adv_opts">
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147 <param name="force" value="false"/>
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148 <param name="test" value="true"/>
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149 </section>
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150 <param name="in" value="MapNormalizer_output.mzML"/>
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151 <param name="read_method" value="indexed_parallel"/>
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152 <param name="loadData" value="true"/>
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153 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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154 <output name="ctd_out" ftype="xml">
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155 <assert_contents>
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156 <is_valid_xml/>
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157 </assert_contents>
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158 </output>
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159 <assert_stdout>
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160 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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161 </assert_stdout>
13
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162 </test>
9
32667824b653 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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163 </tests>
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164 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
0
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165
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166
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167 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TICCalculator.html]]></help>
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168 <expand macro="references"/>
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169 </tool>