Mercurial > repos > galaxyp > openms_highresprecursormasscorrector
diff HighResPrecursorMassCorrector.xml @ 16:b606d4a12558 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 21:40:04 +0000 |
parents | d3546bb9fd8e |
children |
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--- a/HighResPrecursorMassCorrector.xml Thu Dec 01 19:01:37 2022 +0000 +++ b/HighResPrecursorMassCorrector.xml Fri Jun 14 21:40:04 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: [Mass Correction and Calibration]--> <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> + <description>Corrects the precursor mass and charge determined by the instrument software</description> <macros> <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token> <import>macros.xml</import> @@ -15,14 +14,14 @@ ## 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($in.ext)' && mkdir out && #if "out_csv_FLAG" in str($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($feature.in.ext)' && + cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' && #end if ## Main program call @@ -60,32 +59,32 @@ <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)"/> + <param argument="-in" type="data" format="mzml" 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=""> + <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" 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" 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="rt_tolerance" argument="-feature:rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/> + <param name="max_trace" argument="-feature:max_trace" type="integer" 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=""> + <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" 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" 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=""> + <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" 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" 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"/> @@ -93,7 +92,7 @@ </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=""> + <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> @@ -111,14 +110,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_HighResPrecursorMassCorrector_1 --> + <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"/> + <output name="out" value="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"/> @@ -143,39 +143,9 @@ <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> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_HighResPrecursorMassCorrector_3 --> <test expect_num_outputs="2"> @@ -184,7 +154,7 @@ <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"/> + <output name="out" value="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"/> @@ -209,6 +179,9 @@ <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_HighResPrecursorMassCorrector_4 --> <test expect_num_outputs="2"> @@ -217,7 +190,7 @@ <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"/> + <output name="out" value="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"/> @@ -242,6 +215,9 @@ <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_HighResPrecursorMassCorrector_5 --> <test expect_num_outputs="2"> @@ -250,7 +226,7 @@ <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"/> + <output name="out" value="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"/> @@ -275,6 +251,9 @@ <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_HighResPrecursorMassCorrector_6 --> <test expect_num_outputs="2"> @@ -283,7 +262,7 @@ <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"/> + <output name="out" value="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"/> @@ -307,11 +286,14 @@ <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[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> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help> <expand macro="references"/> </tool>