Mercurial > repos > galaxyp > openms_featurefindermetabo
diff FeatureFinderMetabo.xml @ 15:2451315543f9 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 19:24:19 +0000 |
parents | 00080bb4299e |
children | a49dde5a836e |
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--- a/FeatureFinderMetabo.xml Fri Nov 06 19:50:42 2020 +0000 +++ b/FeatureFinderMetabo.xml Thu Dec 01 19:24:19 2022 +0000 @@ -1,13 +1,11 @@ <?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: [Quantitation]--> -<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description> <macros> <token name="@EXECUTABLE@">FeatureFinderMetabo</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -54,7 +52,7 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> <section name="common" title="Common parameters for all other subsections" help="" expanded="false"> <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/> @@ -64,16 +62,16 @@ <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false"> <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/> <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/> - <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace"> + <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace"> <option value="area" selected="true">area</option> <option value="median">median</option> <option value="max_height">max_height</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="quant_method"/> </param> - <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold"> + <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold"> <option value="outlier" selected="true">outlier</option> <option value="sample_rate">sample_rate</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="trace_termination_criterion"/> </param> <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/> <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/> @@ -82,11 +80,11 @@ </section> <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false"> <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/> - <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution"> + <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution"> <option value="off">off</option> <option value="fixed" selected="true">fixed</option> <option value="auto">auto</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="width_filtering"/> </param> <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> @@ -99,12 +97,12 @@ <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/> <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/> <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/> - <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" display="radio" type="select" optional="false" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device"> + <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="true" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device"> <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> <option value="peptides">peptides</option> <option value="none">none</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="isotope_filtering_model"/> </param> <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/> <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/> @@ -112,14 +110,14 @@ <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/> <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/> <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="elements"/> </param> </section> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <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"> @@ -136,13 +134,282 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FeatureFinderMetabo"/> - <expand macro="manutest_FeatureFinderMetabo"/> + <tests><!-- TOPP_FeatureFinderMetabo_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="FeatureFinderMetabo_1_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="300.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="false"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </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_FeatureFinderMetabo_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="FeatureFinderMetabo_2_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="100.0"/> + <param name="chrom_peak_snr" value="0.0"/> + <param name="chrom_fwhm" value="100.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="median"/> + <param name="trace_termination_criterion" value="sample_rate"/> + <param name="trace_termination_outliers" value="2"/> + <param name="min_sample_rate" value="0.01"/> + <param name="min_trace_length" value="30.0"/> + <param name="max_trace_length" value="3000.0"/> + </section> + <section name="epd"> + <param name="enabled" value="false"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="10.0"/> + <param name="max_fwhm" value="80.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="4.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="false"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="false"/> + <param name="use_smoothed_intensities" value="false"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </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_FeatureFinderMetabo_3 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="-1.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="fixed"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FeatureFinderMetabo_4 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="5.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="area"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="-1.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="fixed"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="none"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="true"/> + <param name="remove_single_traces" value="true"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_FeatureFinderMetabo_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="FeatureFinderMetabo_1_input.mzML"/> + <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <section name="algorithm"> + <section name="common"> + <param name="noise_threshold_int" value="10.0"/> + <param name="chrom_peak_snr" value="3.0"/> + <param name="chrom_fwhm" value="5.0"/> + </section> + <section name="mtd"> + <param name="mass_error_ppm" value="20.0"/> + <param name="reestimate_mt_sd" value="true"/> + <param name="quant_method" value="max_height"/> + <param name="trace_termination_criterion" value="outlier"/> + <param name="trace_termination_outliers" value="5"/> + <param name="min_sample_rate" value="0.5"/> + <param name="min_trace_length" value="5.0"/> + <param name="max_trace_length" value="300.0"/> + </section> + <section name="epd"> + <param name="enabled" value="true"/> + <param name="width_filtering" value="off"/> + <param name="min_fwhm" value="3.0"/> + <param name="max_fwhm" value="60.0"/> + <param name="masstrace_snr_filtering" value="false"/> + </section> + <section name="ffm"> + <param name="local_rt_range" value="10.0"/> + <param name="local_mz_range" value="6.5"/> + <param name="charge_lower_bound" value="1"/> + <param name="charge_upper_bound" value="3"/> + <param name="report_summed_ints" value="false"/> + <param name="enable_RT_filtering" value="true"/> + <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> + <param name="mz_scoring_13C" value="true"/> + <param name="use_smoothed_intensities" value="true"/> + <param name="report_convex_hulls" value="false"/> + <param name="remove_single_traces" value="false"/> + <param name="mz_scoring_by_elements" value="false"/> + <param name="elements" value="CHNOPS"/> + </section> + </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[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMetabo.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help> <expand macro="references"/> </tool>