Mercurial > repos > galaxyp > openms_highresprecursormasscorrector
view HighResPrecursorMassCorrector.xml @ 15:d3546bb9fd8e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:01:37 +0000 |
parents | cdbd06d8cbd5 |
children | b606d4a12558 |
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<?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="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Corrects the precursor mass and charge determined by the instrument software.</description> <macros> <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</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($in.ext)' && mkdir out && #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_csv && #end if #if $feature.in: mkdir feature.in && ln -s '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' && #end if ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__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")}' #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_csv 'out_csv/output.${gxy2omsext("csv")}' #end if #if $feature.in: -feature:in 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("mzml")}' '$out' #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv' #end if #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 file (centroided data)" help=" select mzml data sets(s)"/> <section name="feature" title="Use features for precursor mass correction" help="" expanded="false"> <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/> <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/> <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mz_tolerance_unit"/> </param> <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/> <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/> <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/> <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/> <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/> </section> <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false"> <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/> <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mz_tolerance_unit"/> </param> </section> <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false"> <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/> <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mz_tolerance_unit"/> </param> </section> <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=""> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="out_csv_FLAG">out_csv (Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see corresponding subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ)</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"> <filter>OPTIONAL_OUTPUTS is not None and "out_csv_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_HighResPrecursorMassCorrector_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="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> <param name="mz_tolerance" value="5.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="2"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </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_HighResPrecursorMassCorrector_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="4"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </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_HighResPrecursorMassCorrector_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> <param name="mz_tolerance" value="5.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="2"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </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_HighResPrecursorMassCorrector_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> <param name="mz_tolerance" value="5.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="2"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </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_HighResPrecursorMassCorrector_5 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> <param name="mz_tolerance" value="5.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="2"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </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_HighResPrecursorMassCorrector_6 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <section name="feature"> <param name="mz_tolerance" value="5.0"/> <param name="mz_tolerance_unit" value="ppm"/> <param name="rt_tolerance" value="0.0"/> <param name="max_trace" value="2"/> <param name="believe_charge" value="false"/> <param name="keep_original" value="false"/> <param name="assign_all_matching" value="false"/> </section> <section name="nearest_peak"> <param name="mz_tolerance" value="0.0"/> <param name="mz_tolerance_unit" value="ppm"/> </section> <section name="highest_intensity_peak"> <param name="mz_tolerance" value="0.2"/> <param name="mz_tolerance_unit" value="ppm"/> </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[Corrects the precursor mass and charge determined by the instrument software. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help> <expand macro="references"/> </tool>