Mercurial > repos > galaxyp > openms_spectrafilternormalizer
diff SpectraFilterNormalizer.xml @ 13:e4f9ce9d90ad draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:10:52 +0000 |
parents | d736764156d9 |
children | 4ba7fb47318c |
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--- a/SpectraFilterNormalizer.xml Fri Nov 06 19:54:46 2020 +0000 +++ b/SpectraFilterNormalizer.xml Thu Dec 01 19:10:52 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: [Identification]--> -<tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Normalizes intensity of peak spectra.</description> <macros> <token name="@EXECUTABLE@">SpectraFilterNormalizer</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,18 +39,18 @@ <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 file" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> - <param name="method" argument="-algorithm:method" display="radio" type="select" optional="false" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum"> + <param name="method" argument="-algorithm:method" type="select" optional="true" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum"> <option value="to_one" selected="true">to_one</option> <option value="to_TIC">to_TIC</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="method"/> </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"> @@ -65,13 +63,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_SpectraFilterNormalizer"/> - <expand macro="manutest_SpectraFilterNormalizer"/> - </tests> + <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> + <param name="adv_opts|test" value="true"/> + <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> + <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> + </test> +</tests> <help><![CDATA[Normalizes intensity of peak spectra. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraFilterNormalizer.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html]]></help> <expand macro="references"/> </tool>