Mercurial > repos > galaxyp > openms_featurefindercentroided
diff FeatureFinderCentroided.xml @ 0:7dd3b4327a17 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:29:02 -0500 |
| parents | |
| children | 9e6a24fc4f4a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FeatureFinderCentroided.xml Wed Mar 01 12:29:02 2017 -0500 @@ -0,0 +1,167 @@ +<?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 CTD2Galaxy.--> +<!--Proposed Tool Section: [Quantitation]--> +<tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.1.0"> + <description>Detects two-dimensional features in LC-MS data.</description> + <macros> + <token name="@EXECUTABLE@">FeatureFinderCentroided</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FeatureFinderCentroided + +#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 +#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 +#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 $param_algorithm_feature_reported_mz +#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 +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#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 +#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 $adv_opts.param_algorithm_feature_rt_shape +#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 +</command> + <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> + <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"/> + </outputs> + <help>Detects two-dimensional features in LC-MS data. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help> +</tool>