Mercurial > repos > galaxyp > openms_featurefindercentroided
diff FeatureFinderCentroided.xml @ 11:6eda2adf7613 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 03 Sep 2020 16:17:06 +0000 |
| parents | c56b544a3fb2 |
| children | b57f420a47b9 |
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--- a/FeatureFinderCentroided.xml Fri May 17 09:39:03 2019 -0400 +++ b/FeatureFinderCentroided.xml Thu Sep 03 16:17:06 2020 +0000 @@ -1,178 +1,151 @@ <?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="2.3.0"> +<tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <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="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FeatureFinderCentroided + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_seeds: - -seeds $param_seeds -#end if -#if $param_out_mzq: - -out_mzq $param_out_mzq +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && +#if $seeds: + mkdir seeds && + ln -s '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' && #end if -#if $param_algorithm_intensity_bins: - -algorithm:intensity:bins $param_algorithm_intensity_bins -#end if -#if $param_algorithm_mass_trace_mz_tolerance: - -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance -#end if -#if $param_algorithm_mass_trace_min_spectra: - -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra -#end if -#if $param_algorithm_mass_trace_max_missing: - -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing -#end if -#if $param_algorithm_mass_trace_slope_bound: - -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound -#end if -#if $param_algorithm_isotopic_pattern_charge_low: - -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low -#end if -#if $param_algorithm_isotopic_pattern_charge_high: - -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high +#if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_mzq && #end if -#if $param_algorithm_isotopic_pattern_mz_tolerance: - -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance -#end if -#if $param_algorithm_seed_min_score: - -algorithm:seed:min_score $param_algorithm_seed_min_score -#end if -#if $param_algorithm_feature_min_score: - -algorithm:feature:min_score $param_algorithm_feature_min_score -#end if -#if $param_algorithm_feature_reported_mz: - -algorithm:feature:reported_mz - #if " " in str($param_algorithm_feature_reported_mz): - "$param_algorithm_feature_reported_mz" - #else - $param_algorithm_feature_reported_mz - #end if + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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("featurexml")}' +#if $seeds: + -seeds + 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' #end if -#if $param_algorithm_user_seed_rt_tolerance: - -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance -#end if -#if $param_algorithm_user_seed_mz_tolerance: - -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance -#end if -#if $param_algorithm_user_seed_min_score: - -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score +#if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_mzq + 'out_mzq/output.${gxy2omsext("mzq")}' #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if - #if $adv_opts.param_algorithm_debug_pseudo_rt_shift: - -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift -#end if - #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage: - -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage -#end if - #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional: - -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional + +## Postprocessing +&& mv 'out/output.${gxy2omsext("featurexml")}' '$out' +#if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out_mzq/output.${gxy2omsext("mzq")}' '$out_mzq' #end if - #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement: - -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement -#end if - #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width: - -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width -#end if - #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C: - -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C -#end if - #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N: - -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N -#end if - #if $adv_opts.param_algorithm_fit_max_iterations: - -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations -#end if - #if $adv_opts.param_algorithm_feature_min_isotope_fit: - -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit -#end if - #if $adv_opts.param_algorithm_feature_min_trace_score: - -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score -#end if - #if $adv_opts.param_algorithm_feature_min_rt_span: - -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span -#end if - #if $adv_opts.param_algorithm_feature_max_rt_span: - -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span -#end if - #if $adv_opts.param_algorithm_feature_rt_shape: - -algorithm:feature:rt_shape - #if " " in str($adv_opts.param_algorithm_feature_rt_shape): - "$adv_opts.param_algorithm_feature_rt_shape" - #else - $adv_opts.param_algorithm_feature_rt_shape - #end if -#end if - #if $adv_opts.param_algorithm_feature_max_intersection: - -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection -#end if -#end if --threads "\${GALAXY_SLOTS:-1}" -]]></command> +#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 name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> - <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/> - <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. <br>This parameter should be decreased, if the algorithm is used on small regions of a map"/> - <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/> - <param name="param_algorithm_mass_trace_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help="(-min_spectra) "/> - <param name="param_algorithm_mass_trace_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="(-max_missing) <br>This parameter should be well below 'min_spectra'!"/> - <param name="param_algorithm_mass_trace_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="(-slope_bound) <br>This parameter is important to seperate overlapping elution peaks. <br>It should be increased if feature elution profiles fluctuate a lot"/> - <param name="param_algorithm_isotopic_pattern_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search fo" help="(-charge_low) "/> - <param name="param_algorithm_isotopic_pattern_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search fo" help="(-charge_high) "/> - <param name="param_algorithm_isotopic_pattern_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/> - <param name="param_algorithm_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="(-min_score) <br>The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. <br>If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/> - <param name="param_algorithm_feature_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported" help="(-min_score) <br>The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/> - <param name="param_algorithm_feature_reported_mz" display="radio" type="select" optional="False" value="monoisotopic" label="The mass type that is reported for features" help="(-reported_mz) <br>'maximum' returns the m/z value of the highest mass trace. <br>'average' returns the intensity-weighted average m/z value of all contained peaks. <br>'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> + <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)"/> + <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=""/> + </section> + <section name="intensity" title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)" help="" expanded="false"> + <param name="bins" argument="-algorithm:intensity:bins" type="integer" optional="true" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/> + </section> + <section name="mass_trace" title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)" help="" expanded="false"> + <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"/> + </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=""/> + <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" optional="true" min="1" value="4" label="Highest charge to search fo" help=""/> + <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" 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="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" optional="true" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/> + <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" optional="true" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/> + <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" optional="true" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/> + <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" optional="true" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/> + <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" optional="true" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/> + <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" optional="true" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/> + </section> + <section name="seed" title="Settings that determine which peaks are considered a seed" help="" expanded="false"> + <param name="min_score" argument="-algorithm:seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/> + </section> + <section name="fit" title="Settings for the model fitting" help="" expanded="false"> + <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" optional="true" min="1" value="500" label="Maximum number of iterations of the fit" help=""/> + </section> + <section name="feature" title="Settings for the features (intensity, quality assessment, ...)" help="" expanded="false"> + <param name="min_score" argument="-algorithm:feature:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/> + <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/> + <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"> + <option value="symmetric" selected="true">symmetric</option> + <option value="asymmetric">asymmetric</option> + <expand macro="list_string_san"/> + </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"> + <option value="maximum">maximum</option> + <option value="average">average</option> + <option value="monoisotopic" selected="true">monoisotopic</option> + <expand macro="list_string_san"/> + </param> + </section> + <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false"> + <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/> + <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" optional="true" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/> + <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/> + </section> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="out_mzq_FLAG">out_mzq (Overwrites 'seed:min_score' for user-specified seeds)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_algorithm_user_seed_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help="(-rt_tolerance) "/> - <param name="param_algorithm_user_seed_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help="(-mz_tolerance) "/> - <param name="param_algorithm_user_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="(-min_score) The cutoff is typically a bit lower in this case"/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - <param name="param_algorithm_debug_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when" help="(-pseudo_rt_shift) "/> - <param name="param_algorithm_isotopic_pattern_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help="(-intensity_percentage) "/> - <param name="param_algorithm_isotopic_pattern_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help="(-intensity_percentage_optional) "/> - <param name="param_algorithm_isotopic_pattern_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help="(-optional_fit_improvement) "/> - <param name="param_algorithm_isotopic_pattern_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help="(-mass_window_width) "/> - <param name="param_algorithm_isotopic_pattern_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel" help="(-abundance_12C) abundance of the light carbon. Modify if labeled"/> - <param name="param_algorithm_isotopic_pattern_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel" help="(-abundance_14N) abundance of the light nitrogen. Modify if labeled"/> - <param name="param_algorithm_fit_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit" help="(-max_iterations) "/> - <param name="param_algorithm_feature_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting" help="(-min_isotope_fit) "/> - <param name="param_algorithm_feature_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold" help="(-min_trace_score) <br>Traces below this threshold are removed after the model fitting. <br>This parameter is important for features that overlap in m/z dimension"/> - <param name="param_algorithm_feature_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help="(-min_rt_span) "/> - <param name="param_algorithm_feature_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help="(-max_rt_span) "/> - <param name="param_algorithm_feature_rt_shape" display="radio" type="select" optional="False" value="symmetric" label="Choose model used for RT profile fitting" help="(-rt_shape) 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> - </param> - <param name="param_algorithm_feature_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features" help="(-max_intersection) "/> - </expand> </inputs> <outputs> - <data name="param_out" format="featurexml"/> - <data name="param_out_mzq" format="mzq"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> + <data name="out_mzq" label="${tool.name} on ${on_string}: out_mzq" format="mzq"> + <filter>OPTIONAL_OUTPUTS is not None and "out_mzq_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Detects two-dimensional features in LC-MS data. + <tests> + <expand macro="autotest_FeatureFinderCentroided"/> + <expand macro="manutest_FeatureFinderCentroided"/> + </tests> + <help><![CDATA[Detects two-dimensional features in LC-MS data. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderCentroided.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderCentroided.html]]></help> + <expand macro="references"/> </tool>