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view 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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<!--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: [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> <macros> <token name="@EXECUTABLE@">NoiseFilterGaussian</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing mkdir in && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${gxy2omsext("mzml")}' ## Postprocessing && mv 'out/output.${gxy2omsext("mzml")}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> <configfiles> <inputs name="args_json" data_style="paths"/> <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" 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" 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" 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests> <!-- TOPP_NoiseFilterGaussian_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="processOption" value="inmemory"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_1_input.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"/> <param name="use_ppm_tolerance" value="false"/> <param name="write_log_messages" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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"> <section name="adv_opts"> <param name="processOption" value="inmemory"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_2_input.chrom.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"/> <param name="use_ppm_tolerance" value="false"/> <param name="write_log_messages" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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"> <section name="adv_opts"> <param name="processOption" value="lowmemory"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_1_input.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"/> <param name="use_ppm_tolerance" value="false"/> <param name="write_log_messages" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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"> <section name="adv_opts"> <param name="processOption" value="lowmemory"/> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="NoiseFilterGaussian_2_input.chrom.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"/> <param name="use_ppm_tolerance" value="false"/> <param name="write_log_messages" value="false"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <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 https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterGaussian.html]]></help> <expand macro="references"/> </tool>