Mercurial > repos > galaxyp > openms_metabolitespectralmatcher

comparison MetaboliteSpectralMatcher.xml @ 13:75ccdbc2475d 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 19:02:30 +0000
parents d8503d5dd2ba
children e46a9e72c395
comparison
equal deleted inserted replaced
12:6f98f87751ff 13:75ccdbc2475d
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Perform a spectral library search.</description> 5 <description>Perform a spectral library search.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token> 7 <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</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 spectra" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/>
49 <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/> 47 <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml 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="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/> 49 <param name="prec_mass_error_value" argument="-algorithm:prec_mass_error_value" type="float" optional="true" value="100.0" label="Error allowed for precursor ion mass" help=""/>
52 <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/> 50 <param name="frag_mass_error_value" argument="-algorithm:frag_mass_error_value" type="float" optional="true" value="500.0" label="Error allowed for product ions" help=""/>
53 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" display="radio" type="select" optional="false" label="Unit of mass error (ppm or Da)" help=""> 51 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
54 <option value="ppm" selected="true">ppm</option> 52 <option value="ppm" selected="true">ppm</option>
55 <option value="Da">Da</option> 53 <option value="Da">Da</option>
56 <expand macro="list_string_san"/> 54 <expand macro="list_string_san" name="mass_error_unit"/>
57 </param> 55 </param>
58 <param name="report_mode" argument="-algorithm:report_mode" display="radio" type="select" optional="false" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help=""> 56 <param name="report_mode" argument="-algorithm:report_mode" type="select" optional="true" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="">
59 <option value="top3" selected="true">top3</option> 57 <option value="top3" selected="true">top3</option>
60 <option value="best">best</option> 58 <option value="best">best</option>
61 <expand macro="list_string_san"/> 59 <expand macro="list_string_san" name="report_mode"/>
62 </param> 60 </param>
63 <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help=""> 61 <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help="">
64 <option value="positive" selected="true">positive</option> 62 <option value="positive" selected="true">positive</option>
65 <option value="negative">negative</option> 63 <option value="negative">negative</option>
66 <expand macro="list_string_san"/> 64 <expand macro="list_string_san" name="ionization_mode"/>
67 </param> 65 </param>
68 </section> 66 </section>
69 <expand macro="adv_opts_macro"> 67 <expand macro="adv_opts_macro">
70 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 68 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
71 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 69 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
72 <expand macro="list_string_san"/> 70 <expand macro="list_string_san" name="test"/>
73 </param> 71 </param>
74 </expand> 72 </expand>
75 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 73 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
76 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 74 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
77 </param> 75 </param>
80 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 78 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
81 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 79 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
82 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 80 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
83 </data> 81 </data>
84 </outputs> 82 </outputs>
85 <tests> 83 <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
86 <expand macro="autotest_MetaboliteSpectralMatcher"/> 84 <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
87 <expand macro="manutest_MetaboliteSpectralMatcher"/> 85 <param name="adv_opts|test" value="true"/>
88 </tests> 86 <param name="in" ftype="mzml" value="spectra.mzML"/>
87 <param name="database" value="MetaboliteSpectralDB.mzML"/>
88 <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
89 </test>
90 </tests>
89 <help><![CDATA[Perform a spectral library search. 91 <help><![CDATA[Perform a spectral library search.
90 92
91 93
92 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help> 94 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help>
93 <expand macro="references"/> 95 <expand macro="references"/>
94 </tool> 96 </tool>