Mercurial > repos > galaxyp > openms_mrmmapper

annotate MRMMapper.xml @ 14:47f82df5bdea 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 21:45:15 +0000
parents 9a6f6a0ed604
children
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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: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">MRMMapper</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($in.ext)' &&
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18 mkdir tr &&
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19 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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20 mkdir out &&
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22 ## Main program call
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24 set -o pipefail &&
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25 @EXECUTABLE@ -write_ctd ./ &&
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26 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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27 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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28 -in
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29 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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30 -tr
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31 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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32 -out
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33 'out/output.${gxy2omsext("mzml")}'
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35 ## Postprocessing
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36 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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38 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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39 #end if]]></command>
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40 <configfiles>
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41 <inputs name="args_json" data_style="paths"/>
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42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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43 </configfiles>
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44 <inputs>
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45 <param argument="-in" type="data" format="mzml" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
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46 <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
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47 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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48 <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
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49 <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
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50 <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/>
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51 <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
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52 </section>
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53 <expand macro="adv_opts_macro">
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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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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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 ${on_string}: out" format="mzml"/>
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65 <data name="ctd_out" format="xml" label="${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_MRMMapper_test_1 -->
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71 <test expect_num_outputs="2">
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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="MRMMapping_input.chrom.mzML"/>
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77 <param name="tr" value="MRMMapping_input.TraML"/>
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78 <output name="out" value="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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79 <section name="algorithm">
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80 <param name="precursor_tolerance" value="0.3"/>
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81 <param name="product_tolerance" value="0.3"/>
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82 <param name="map_multiple_assays" value="false"/>
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83 <param name="error_on_unmapped" value="false"/>
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84 </section>
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85 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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86 <output name="ctd_out" ftype="xml">
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87 <assert_contents>
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88 <is_valid_xml/>
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89 </assert_contents>
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90 </output>
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91 <assert_stdout>
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92 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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93 </assert_stdout>
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94 </test>
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95 <!-- TOPP_MRMMapper_test_2 -->
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96 <test expect_num_outputs="2">
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97 <section name="adv_opts">
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98 <param name="force" value="false"/>
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99 <param name="test" value="true"/>
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100 </section>
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101 <param name="in" value="MRMMapping_input.chrom.mzML"/>
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102 <param name="tr" value="MRMMapping_input_2.TraML"/>
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103 <output name="out" value="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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104 <section name="algorithm">
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105 <param name="precursor_tolerance" value="0.01"/>
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106 <param name="product_tolerance" value="0.01"/>
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107 <param name="map_multiple_assays" value="false"/>
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108 <param name="error_on_unmapped" value="false"/>
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109 </section>
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110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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111 <output name="ctd_out" ftype="xml">
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112 <assert_contents>
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113 <is_valid_xml/>
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114 </assert_contents>
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115 </output>
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116 <assert_stdout>
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117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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118 </assert_stdout>
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119 </test>
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120 </tests>
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121 <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
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122
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123
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124 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMMapper.html]]></help>
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125 <expand macro="references"/>
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126 </tool>