Mercurial > repos > galaxyp > openms_noisefiltersgolay
view NoiseFilterSGolay.xml @ 13:cf86c9091cb3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:05:55 +0000 |
parents | 1312f9119f74 |
children | 35468667de97 |
line wrap: on
line source
<?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]--> <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> <macros> <token name="@EXECUTABLE@">NoiseFilterSGolay</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 && ln -s '$in' 'in/${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" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" 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=""> <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=""> <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_NoiseFilterSGolay_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="NoiseFilterSGolay_1_input.mzML"/> <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="frame_length" value="9"/> <param name="polynomial_order" value="4"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_NoiseFilterSGolay_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="NoiseFilterSGolay_2_input.chrom.mzML"/> <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="frame_length" value="11"/> <param name="polynomial_order" value="4"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_NoiseFilterSGolay_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="NoiseFilterSGolay_1_input.mzML"/> <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="frame_length" value="9"/> <param name="polynomial_order" value="4"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_NoiseFilterSGolay_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="NoiseFilterSGolay_2_input.chrom.mzML"/> <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="algorithm"> <param name="frame_length" value="11"/> <param name="polynomial_order" value="4"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> </tests> <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help> <expand macro="references"/> </tool>