Mercurial > repos > galaxyp > openms_featurefindercentroided
diff FeatureFinderCentroided.xml @ 15:1a709ba66f2f draft default tip
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 18:57:17 +0000 |
parents | b57f420a47b9 |
children |
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--- a/FeatureFinderCentroided.xml Fri Nov 06 20:20:54 2020 +0000 +++ b/FeatureFinderCentroided.xml Thu Dec 01 18:57:17 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="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Detects two-dimensional features in LC-MS data.</description> <macros> <token name="@EXECUTABLE@">FeatureFinderCentroided</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -62,8 +60,8 @@ <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="input file" help=" select mzml data sets(s)"/> - <param name="seeds" argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> + <param argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/> <section name="algorithm" title="Algorithm section" help="" expanded="false"> <section name="debug" title="" help="" expanded="false"> <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" optional="true" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/> @@ -75,7 +73,7 @@ <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/> <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" optional="true" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/> <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" optional="true" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/> - <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to seperate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/> + <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to separate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/> </section> <section name="isotopic_pattern" title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)" help="" expanded="false"> <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" optional="true" min="1" value="1" label="Lowest charge to search fo" help=""/> @@ -100,17 +98,17 @@ <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/> <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="true" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/> <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="true" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/> - <param name="rt_shape" argument="-algorithm:feature:rt_shape" display="radio" type="select" optional="false" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used"> + <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" optional="true" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used"> <option value="symmetric" selected="true">symmetric</option> <option value="asymmetric">asymmetric</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="rt_shape"/> </param> <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="true" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/> - <param name="reported_mz" argument="-algorithm:feature:reported_mz" display="radio" type="select" optional="false" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model"> + <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" optional="true" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model"> <option value="maximum">maximum</option> <option value="average">average</option> <option value="monoisotopic" selected="true">monoisotopic</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="reported_mz"/> </param> </section> <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false"> @@ -120,9 +118,9 @@ </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"> @@ -139,13 +137,69 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FeatureFinderCentroided"/> - <expand macro="manutest_FeatureFinderCentroided"/> + <tests><!-- TOPP_FeatureFinderCentroided_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + <param name="pseudo_rt_shift" value="500.0"/> + </section> + <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> + <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <section name="algorithm"> + <section name="intensity"> + <param name="bins" value="1"/> + </section> + <section name="mass_trace"> + <param name="mz_tolerance" value="0.02"/> + <param name="min_spectra" value="14"/> + <param name="max_missing" value="1"/> + <param name="slope_bound" value="0.1"/> + </section> + <section name="isotopic_pattern"> + <param name="charge_low" value="2"/> + <param name="charge_high" value="2"/> + <param name="mz_tolerance" value="0.02"/> + <param name="intensity_percentage" value="10.0"/> + <param name="intensity_percentage_optional" value="0.1"/> + <param name="optional_fit_improvement" value="2.0"/> + <param name="mass_window_width" value="100.0"/> + <param name="abundance_12C" value="98.93"/> + <param name="abundance_14N" value="99.632"/> + </section> + <section name="seed"> + <param name="min_score" value="0.8"/> + </section> + <section name="fit"> + <param name="max_iterations" value="500"/> + </section> + <section name="feature"> + <param name="min_score" value="0.7"/> + <param name="min_isotope_fit" value="0.8"/> + <param name="min_trace_score" value="0.5"/> + <param name="min_rt_span" value="0.333"/> + <param name="max_rt_span" value="2.5"/> + <param name="rt_shape" value="symmetric"/> + <param name="max_intersection" value="0.35"/> + <param name="reported_mz" value="monoisotopic"/> + </section> + <section name="user-seed"> + <param name="rt_tolerance" value="5.0"/> + <param name="mz_tolerance" value="1.1"/> + <param name="min_score" value="0.5"/> + </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[Detects two-dimensional features in LC-MS data. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderCentroided.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderCentroided.html]]></help> <expand macro="references"/> </tool>