Mercurial > repos > galaxyp > openms_noisefiltergaussian
diff NoiseFilterGaussian.xml @ 14:464f7877215b draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:37:30 +0000 |
parents | 47982606f542 |
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--- a/NoiseFilterGaussian.xml Thu Dec 01 19:19:06 2022 +0000 +++ b/NoiseFilterGaussian.xml Fri Jun 14 21:37:30 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="NoiseFilterGaussian" name="NoiseFilterGaussian" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).</description> + <description>Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data)</description> <macros> <token name="@EXECUTABLE@">NoiseFilterGaussian</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 @@ -39,21 +38,21 @@ <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="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> - <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" optional="true" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/> - <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" optional="true" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/> + <param name="gaussian_width" argument="-algorithm:gaussian_width" type="float" value="0.2" label="Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z)" help=""/> + <param name="ppm_tolerance" argument="-algorithm:ppm_tolerance" type="float" value="10.0" label="Gaussian width, depending on the m/z position" help="The higher the value, the wider the peak and therefore the wider the gaussian"/> <param name="use_ppm_tolerance" argument="-algorithm:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, instead of the gaussian_width value, the ppm_tolerance is used" help="The gaussian is calculated in each step anew, so this is much slower"/> <param name="write_log_messages" argument="-algorithm:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="true: Warn if no signal was found by the Gauss filter algorithm" help=""/> </section> <expand macro="adv_opts_macro"> - <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help=""> + <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help=""> <option value="inmemory" selected="true">inmemory</option> <option value="lowmemory">lowmemory</option> <expand macro="list_string_san" name="processOption"/> </param> <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> @@ -67,7 +66,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_NoiseFilterGaussian_1 --> + <tests> + <!-- TOPP_NoiseFilterGaussian_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="processOption" value="inmemory"/> @@ -75,7 +75,7 @@ <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="gaussian_width" value="1.0"/> <param name="ppm_tolerance" value="10.0"/> @@ -88,6 +88,9 @@ <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> <!-- TOPP_NoiseFilterGaussian_2 --> <test expect_num_outputs="2"> @@ -97,7 +100,7 @@ <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="gaussian_width" value="50.0"/> <param name="ppm_tolerance" value="10.0"/> @@ -110,6 +113,9 @@ <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> <!-- TOPP_NoiseFilterGaussian_3 --> <test expect_num_outputs="2"> @@ -119,7 +125,7 @@ <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="gaussian_width" value="1.0"/> <param name="ppm_tolerance" value="10.0"/> @@ -132,6 +138,9 @@ <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> <!-- TOPP_NoiseFilterGaussian_4 --> <test expect_num_outputs="2"> @@ -141,7 +150,7 @@ <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="gaussian_width" value="50.0"/> <param name="ppm_tolerance" value="10.0"/> @@ -154,11 +163,14 @@ <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 noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterGaussian.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterGaussian.html]]></help> <expand macro="references"/> </tool>