Mercurial > repos > galaxyp > openms_dtaextractor

annotate DTAExtractor.xml @ 17:79706b7647c3 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 19:17:40 +0000
parents d8b1ec05fbd7
children 78024781d209
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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="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Extracts spectra of an MS run file to several files in DTA format.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DTAExtractor</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 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 ## Main program call
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21
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 | tee '$stdout'
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30 ## Postprocessing
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31 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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32 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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33 #end if]]></command>
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34 <configfiles>
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35 <inputs name="args_json" data_style="paths"/>
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36 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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37 </configfiles>
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38 <inputs>
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39 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
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40 <param argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
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41 <expand macro="list_string_san" name="out"/>
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42 </param>
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43 <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
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44 <expand macro="list_string_san" name="mz"/>
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45 </param>
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46 <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
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47 <expand macro="list_string_san" name="rt"/>
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48 </param>
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49 <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
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50 <expand macro="list_string_san" name="level"/>
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51 </param>
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52 <expand macro="adv_opts_macro">
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53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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54 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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55 <expand macro="list_string_san" name="test"/>
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56 </param>
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57 </expand>
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58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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64 <filter>OPTIONAL_OUTPUTS is None</filter>
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65 </data>
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66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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68 </data>
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69 </outputs>
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70 <tests><!-- 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 </test>
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88 <!-- TOPP_DTAExtractor_2 -->
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89 <test expect_num_outputs="1">
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90 <section name="adv_opts">
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91 <param name="force" value="false"/>
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92 <param name="test" value="true"/>
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93 </section>
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94 <param name="in" value="DTAExtractor_1_input.mzML"/>
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95 <param name="out" value="DTAExtractor"/>
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96 <param name="mz" value=":"/>
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97 <param name="rt" value=":"/>
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98 <param name="level" value="1"/>
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99 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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100 <output name="ctd_out" ftype="xml">
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101 <assert_contents>
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102 <is_valid_xml/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 <!-- TOPP_DTAExtractor_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="DTAExtractor_1_input.mzML"/>
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113 <param name="out" value="DTAExtractor"/>
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114 <param name="mz" value=":1000"/>
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115 <param name="rt" value=":"/>
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116 <param name="level" value="2"/>
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117 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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118 <output name="ctd_out" ftype="xml">
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119 <assert_contents>
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120 <is_valid_xml/>
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121 </assert_contents>
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122 </output>
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123 </test>
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124 </tests>
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125 <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.
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126
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127
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128 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help>
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129 <expand macro="references"/>
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130 </tool>