Mercurial > repos > galaxyp > openms_baselinefilter
diff BaselineFilter.xml @ 18:84bd73e60367 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
---|---|
date | Fri, 14 Jun 2024 21:37:37 +0000 |
parents | ddbae9eb797e |
children |
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--- a/BaselineFilter.xml Thu Dec 01 19:10:21 2022 +0000 +++ b/BaselineFilter.xml Fri Jun 14 21:37:37 2024 +0000 @@ -1,8 +1,7 @@ -<?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: [Signal processing and preprocessing]--> +<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]--> <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Removes the baseline from profile spectra using a top-hat filter.</description> + <description>Removes the baseline from profile spectra using a top-hat filter</description> <macros> <token name="@EXECUTABLE@">BaselineFilter</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,14 +38,14 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> - <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/> - <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help=""> + <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/> + <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/> + <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help=""> <option value="Thomson" selected="true">Thomson</option> <option value="DataPoints">DataPoints</option> <expand macro="list_string_san" name="struc_elem_unit"/> </param> - <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default"> + <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default"> <option value="identity">identity</option> <option value="erosion">erosion</option> <option value="dilation">dilation</option> @@ -61,7 +60,7 @@ </param> <expand macro="adv_opts_macro"> <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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -75,14 +74,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_BaselineFilter_1 --> + <tests> + <!-- TOPP_BaselineFilter_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="BaselineFilter_input.mzML"/> - <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="struc_elem_length" value="1.5"/> <param name="struc_elem_unit" value="Thomson"/> <param name="method" value="tophat"/> @@ -92,11 +92,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help> <expand macro="references"/> </tool>