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comparison MRMMapper.xml @ 13:9a6f6a0ed604 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 19:06:17 +0000
parents bc8e70bada0e
children 47f82df5bdea
comparison
equal deleted inserted replaced
12:a6774479101a 13:9a6f6a0ed604
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description> 5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MRMMapper</token> 7 <token name="@EXECUTABLE@">MRMMapper</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
49 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/> 47 <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
50 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
51 <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/> 49 <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
52 <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/> 50 <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
53 <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=""/> 51 <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=""/>
54 <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=""/> 52 <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=""/>
55 </section> 53 </section>
56 <expand macro="adv_opts_macro"> 54 <expand macro="adv_opts_macro">
57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
59 <expand macro="list_string_san"/> 57 <expand macro="list_string_san" name="test"/>
60 </param> 58 </param>
61 </expand> 59 </expand>
62 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 </param> 62 </param>
67 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data> 68 </data>
71 </outputs> 69 </outputs>
72 <tests> 70 <tests><!-- TOPP_MRMMapper_test_1 -->
73 <expand macro="autotest_MRMMapper"/> 71 <test expect_num_outputs="2">
74 <expand macro="manutest_MRMMapper"/> 72 <section name="adv_opts">
73 <param name="force" value="false"/>
74 <param name="test" value="true"/>
75 </section>
76 <param name="in" value="MRMMapping_input.chrom.mzML"/>
77 <param name="tr" value="MRMMapping_input.TraML"/>
78 <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
79 <section name="algorithm">
80 <param name="precursor_tolerance" value="0.3"/>
81 <param name="product_tolerance" value="0.3"/>
82 <param name="map_multiple_assays" value="false"/>
83 <param name="error_on_unmapped" value="false"/>
84 </section>
85 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
86 <output name="ctd_out" ftype="xml">
87 <assert_contents>
88 <is_valid_xml/>
89 </assert_contents>
90 </output>
91 </test>
92 <!-- TOPP_MRMMapper_test_2 -->
93 <test expect_num_outputs="2">
94 <section name="adv_opts">
95 <param name="force" value="false"/>
96 <param name="test" value="true"/>
97 </section>
98 <param name="in" value="MRMMapping_input.chrom.mzML"/>
99 <param name="tr" value="MRMMapping_input_2.TraML"/>
100 <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
101 <section name="algorithm">
102 <param name="precursor_tolerance" value="0.01"/>
103 <param name="product_tolerance" value="0.01"/>
104 <param name="map_multiple_assays" value="false"/>
105 <param name="error_on_unmapped" value="false"/>
106 </section>
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
108 <output name="ctd_out" ftype="xml">
109 <assert_contents>
110 <is_valid_xml/>
111 </assert_contents>
112 </output>
113 </test>
75 </tests> 114 </tests>
76 <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 115 <help><![CDATA[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
77 116
78 117
79 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MRMMapper.html]]></help> 118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MRMMapper.html]]></help>
80 <expand macro="references"/> 119 <expand macro="references"/>
81 </tool> 120 </tool>