Mercurial > repos > galaxyp > openms_metabolitespectralmatcher
diff MetaboliteSpectralMatcher.xml @ 13:75ccdbc2475d draft default tip
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 |
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--- a/MetaboliteSpectralMatcher.xml Fri Nov 06 20:22:22 2020 +0000 +++ b/MetaboliteSpectralMatcher.xml Thu Dec 01 19:02:30 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Perform a spectral library search.</description> <macros> <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,31 +43,31 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/> - <param name="database" argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="Input spectra" help=" select mzml data sets(s)"/> + <param argument="-database" type="data" format="mzml" optional="false" label="Default spectral database" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> <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=""/> <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=""/> - <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=""> + <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_error_unit"/> </param> - <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=""> + <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=""> <option value="top3" selected="true">top3</option> <option value="best">best</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="report_mode"/> </param> - <param name="ionization_mode" argument="-algorithm:ionization_mode" display="radio" type="select" optional="false" label="Positive or negative ionization mode?" help=""> + <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode?" help=""> <option value="positive" selected="true">positive</option> <option value="negative">negative</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="ionization_mode"/> </param> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -82,13 +80,17 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MetaboliteSpectralMatcher"/> - <expand macro="manutest_MetaboliteSpectralMatcher"/> - </tests> + <tests><!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="spectra.mzML"/> + <param name="database" value="MetaboliteSpectralDB.mzML"/> + <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> + </test> +</tests> <help><![CDATA[Perform a spectral library search. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaboliteSpectralMatcher.html]]></help> <expand macro="references"/> </tool>