Mercurial > repos > galaxyp > openms_erpairfinder
diff ERPairFinder.xml @ 15:d6ef464ff66b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:06:06 +0000 |
| parents | e5e2b0d57f1d |
| children | 3d043a92c582 |
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--- a/ERPairFinder.xml Fri Nov 06 19:57:06 2020 +0000 +++ b/ERPairFinder.xml Thu Dec 01 19:06:06 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="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="ERPairFinder" name="ERPairFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description> <macros> <token name="@EXECUTABLE@">ERPairFinder</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -58,18 +56,18 @@ <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 mzML file containing the ER spectra" help=" select mzml data sets(s)"/> - <param name="pair_in" argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/> - <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/> + <param argument="-in" type="data" format="mzml" optional="false" label="Input mzML file containing the ER spectra" help=" select mzml data sets(s)"/> + <param argument="-pair_in" type="data" format="txt" optional="false" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help=" select txt data sets(s)"/> + <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help=""/> <expand macro="adv_opts_macro"> - <param name="RT_tolerance" argument="-RT_tolerance" type="float" optional="true" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/> - <param name="max_charge" argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/> - <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/> - <param name="max_isotope" argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/> - <param name="expansion_range" argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/> - <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="-RT_tolerance" type="float" optional="true" min="1.0" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help=""/> + <param argument="-max_charge" type="integer" optional="true" min="1" value="3" label="Maximal charge state features should be search fo" help=""/> + <param argument="-intensity_threshold" type="float" optional="true" min="-1.0" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help=""/> + <param argument="-max_isotope" type="integer" optional="true" min="2" value="3" label="Max isotope of the isotope distribution to be considered" help=""/> + <param argument="-expansion_range" type="float" optional="true" min="0.0" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help=""/> + <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"> @@ -86,13 +84,11 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_ERPairFinder"/> - <expand macro="manutest_ERPairFinder"/> - </tests> + <tests><!-- TODO --> +</tests> <help><![CDATA[Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_ERPairFinder.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_ERPairFinder.html]]></help> <expand macro="references"/> </tool>