Mercurial > repos > galaxyp > openms_dtaextractor

annotate DTAExtractor.xml @ 18:78024781d209 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 21:43:05 +0000
parents 79706b7647c3
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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: [File Filtering / Extraction / Merging]-->
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3 <tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Extracts spectra of an MS run file to several files in DTA format</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">DTAExtractor</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($in.ext)' &&
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19 ## Main program call
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20
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21 set -o pipefail &&
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22 @EXECUTABLE@ -write_ctd ./ &&
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23 python3 '$__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="mzml" label="input file" help=" select mzml data sets(s)"/>
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39 <param argument="-out" type="text" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
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40 <expand macro="list_string_san" name="out"/>
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41 </param>
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42 <param argument="-mz" type="text" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
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43 <expand macro="list_string_san" name="mz"/>
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44 </param>
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45 <param argument="-rt" type="text" value=":" label="retention time range of spectra to extract" help="">
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46 <expand macro="list_string_san" name="rt"/>
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47 </param>
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48 <param argument="-level" type="text" value="1,2,3" label="MS levels to extract" help="">
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49 <expand macro="list_string_san" name="level"/>
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50 </param>
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51 <expand macro="adv_opts_macro">
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52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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53 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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54 <expand macro="list_string_san" name="test"/>
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55 </param>
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56 </expand>
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57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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63 <filter>OPTIONAL_OUTPUTS is None</filter>
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64 </data>
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65 <data name="ctd_out" format="xml" label="${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>
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70 <!-- TOPP_DTAExtractor_1 -->
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71 <test expect_num_outputs="1">
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72 <section name="adv_opts">
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73 <param name="force" value="false"/>
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74 <param name="test" value="true"/>
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75 </section>
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76 <param name="in" value="DTAExtractor_1_input.mzML"/>
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77 <param name="out" value="DTAExtractor"/>
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78 <param name="mz" value=":"/>
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79 <param name="rt" value=":61"/>
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80 <param name="level" value="1,2,3"/>
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81 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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82 <output name="ctd_out" ftype="xml">
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83 <assert_contents>
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84 <is_valid_xml/>
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85 </assert_contents>
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86 </output>
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87 <assert_stdout>
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88 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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89 </assert_stdout>
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90 </test>
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91 <!-- TOPP_DTAExtractor_2 -->
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92 <test expect_num_outputs="1">
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93 <section name="adv_opts">
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94 <param name="force" value="false"/>
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95 <param name="test" value="true"/>
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96 </section>
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97 <param name="in" value="DTAExtractor_1_input.mzML"/>
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98 <param name="out" value="DTAExtractor"/>
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99 <param name="mz" value=":"/>
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100 <param name="rt" value=":"/>
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101 <param name="level" value="1"/>
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102 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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103 <output name="ctd_out" ftype="xml">
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104 <assert_contents>
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105 <is_valid_xml/>
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106 </assert_contents>
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107 </output>
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108 <assert_stdout>
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109 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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110 </assert_stdout>
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111 </test>
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112 <!-- TOPP_DTAExtractor_3 -->
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113 <test expect_num_outputs="1">
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114 <section name="adv_opts">
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115 <param name="force" value="false"/>
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116 <param name="test" value="true"/>
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117 </section>
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118 <param name="in" value="DTAExtractor_1_input.mzML"/>
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119 <param name="out" value="DTAExtractor"/>
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120 <param name="mz" value=":1000"/>
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121 <param name="rt" value=":"/>
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122 <param name="level" value="2"/>
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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>
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132 </test>
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133 </tests>
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134 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
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135
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136
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137 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DTAExtractor.html]]></help>
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138 <expand macro="references"/>
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139 </tool>