Mercurial > repos > bgruening > openms
view PeakPickerWavelet.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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<?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: [Signal processing and preprocessing]--> <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.0.0"> <description>Finds mass spectrometric peaks in profile mass spectra.</description> <macros> <token name="@EXECUTABLE@">PeakPickerWavelet</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>PeakPickerWavelet #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_signal_to_noise: -algorithm:signal_to_noise $param_algorithm_signal_to_noise #end if #if $param_algorithm_peak_width: -algorithm:peak_width $param_algorithm_peak_width #end if #if $param_algorithm_estimate_peak_width: -algorithm:estimate_peak_width #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_write_peak_meta_data: -write_peak_meta_data #end if #if $adv_opts.param_force: -force #end if #if $adv_opts.param_algorithm_centroid_percentage: -algorithm:centroid_percentage $adv_opts.param_algorithm_centroid_percentage #end if #if $adv_opts.param_algorithm_fwhm_lower_bound_factor: -algorithm:fwhm_lower_bound_factor $adv_opts.param_algorithm_fwhm_lower_bound_factor #end if #if $adv_opts.param_algorithm_fwhm_upper_bound_factor: -algorithm:fwhm_upper_bound_factor $adv_opts.param_algorithm_fwhm_upper_bound_factor #end if #if $adv_opts.param_algorithm_optimization_iterations: -algorithm:optimization:iterations $adv_opts.param_algorithm_optimization_iterations #end if #if $adv_opts.param_algorithm_optimization_penalties_position: -algorithm:optimization:penalties:position $adv_opts.param_algorithm_optimization_penalties_position #end if #if $adv_opts.param_algorithm_optimization_penalties_left_width: -algorithm:optimization:penalties:left_width $adv_opts.param_algorithm_optimization_penalties_left_width #end if #if $adv_opts.param_algorithm_optimization_penalties_right_width: -algorithm:optimization:penalties:right_width $adv_opts.param_algorithm_optimization_penalties_right_width #end if #if $adv_opts.param_algorithm_optimization_penalties_height: -algorithm:optimization:penalties:height $adv_opts.param_algorithm_optimization_penalties_height #end if #if $adv_opts.param_algorithm_optimization_2d_tolerance_mz: -algorithm:optimization:2d:tolerance_mz $adv_opts.param_algorithm_optimization_2d_tolerance_mz #end if #if $adv_opts.param_algorithm_optimization_2d_max_peak_distance: -algorithm:optimization:2d:max_peak_distance $adv_opts.param_algorithm_optimization_2d_max_peak_distance #end if #if $adv_opts.param_algorithm_thresholds_peak_bound: -algorithm:thresholds:peak_bound $adv_opts.param_algorithm_thresholds_peak_bound #end if #if $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level: -algorithm:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level #end if #if $adv_opts.param_algorithm_thresholds_correlation: -algorithm:thresholds:correlation $adv_opts.param_algorithm_thresholds_correlation #end if #if $adv_opts.param_algorithm_thresholds_noise_level: -algorithm:thresholds:noise_level $adv_opts.param_algorithm_thresholds_noise_level #end if #if $adv_opts.param_algorithm_thresholds_search_radius: -algorithm:thresholds:search_radius $adv_opts.param_algorithm_thresholds_search_radius #end if #if $adv_opts.param_algorithm_wavelet_transform_spacing: -algorithm:wavelet_transform:spacing $adv_opts.param_algorithm_wavelet_transform_spacing #end if #if $adv_opts.param_algorithm_deconvolution_deconvolution: -algorithm:deconvolution:deconvolution #end if #if $adv_opts.param_algorithm_deconvolution_asym_threshold: -algorithm:deconvolution:asym_threshold $adv_opts.param_algorithm_deconvolution_asym_threshold #end if #if $adv_opts.param_algorithm_deconvolution_left_width: -algorithm:deconvolution:left_width $adv_opts.param_algorithm_deconvolution_left_width #end if #if $adv_opts.param_algorithm_deconvolution_right_width: -algorithm:deconvolution:right_width $adv_opts.param_algorithm_deconvolution_right_width #end if #if $adv_opts.param_algorithm_deconvolution_scaling: -algorithm:deconvolution:scaling $adv_opts.param_algorithm_deconvolution_scaling #end if #if $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold: -algorithm:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold #end if #if $adv_opts.param_algorithm_deconvolution_fitting_eps_abs: -algorithm:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_deconvolution_fitting_eps_abs #end if #if $adv_opts.param_algorithm_deconvolution_fitting_eps_rel: -algorithm:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_deconvolution_fitting_eps_rel #end if #if $adv_opts.param_algorithm_deconvolution_fitting_max_iteration: -algorithm:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_deconvolution_fitting_max_iteration #end if #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_position: -algorithm:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_deconvolution_fitting_penalties_position #end if #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_height: -algorithm:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_deconvolution_fitting_penalties_height #end if #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width: -algorithm:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width #end if #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width: -algorithm:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity: -algorithm:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor: -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile: -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode: -algorithm:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len: -algorithm:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count: -algorithm:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp: -algorithm:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements: -algorithm:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements #end if #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window: -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window #end if #end if </command> <inputs> <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/> <param help="(-signal_to_noise) " label="Minimal signal to noise ratio for a peak to be picked" min="0.0" name="param_algorithm_signal_to_noise" optional="True" type="float" value="1.0"/> <param help="(-peak_width) " label="Approximate fwhm of the peaks" min="0.0" name="param_algorithm_peak_width" optional="True" type="float" value="0.15"/> <param checked="false" falsevalue="" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored" label="Flag if the average peak width shall be estimated" name="param_algorithm_estimate_peak_width" optional="True" truevalue="-algorithm:estimate_peak_width" type="boolean"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-write_peak_meta_data) Attention: this can blow up files, since seven arrays are stored per spectrum!" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" name="param_write_peak_meta_data" optional="True" truevalue="-write_peak_meta_data" type="boolean"/> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param help="(-centroid_percentage) If it is 1 the centroid position corresponds to the position of the highest intensity" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" max="1.0" min="0.0" name="param_algorithm_centroid_percentage" optional="True" type="float" value="0.8"/> <param help="(-fwhm_lower_bound_factor) All peaks with width smaller than fwhm_bound_factor * peak_width are discarded" label="Factor that calculates the minimal fwhm value from the peak_width" min="0.0" name="param_algorithm_fwhm_lower_bound_factor" optional="True" type="float" value="0.7"/> <param help="(-fwhm_upper_bound_factor) All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded" label="Factor that calculates the maximal fwhm value from the peak_width" min="0.0" name="param_algorithm_fwhm_upper_bound_factor" optional="True" type="float" value="20.0"/> <param help="(-iterations) " label="maximal number of iterations for the fitting step" min="1" name="param_algorithm_optimization_iterations" optional="True" type="integer" value="400"/> <param help="(-position) " label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" min="0.0" name="param_algorithm_optimization_penalties_position" optional="True" type="float" value="0.0"/> <param help="(-left_width) " label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" min="0.0" name="param_algorithm_optimization_penalties_left_width" optional="True" type="float" value="1.0"/> <param help="(-right_width) " label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" min="0.0" name="param_algorithm_optimization_penalties_right_width" optional="True" type="float" value="1.0"/> <param help="(-height) " label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" min="0.0" name="param_algorithm_optimization_penalties_height" optional="True" type="float" value="1.0"/> <param help="(-tolerance_mz) " label="mz tolerance for cluster construction" min="0.0" name="param_algorithm_optimization_2d_tolerance_mz" optional="True" type="float" value="2.2"/> <param help="(-max_peak_distance) " label="maximal peak distance in mz in a cluste" min="0.0" name="param_algorithm_optimization_2d_max_peak_distance" optional="True" type="float" value="1.2"/> <param help="(-peak_bound) " label="Minimal peak intensity" min="0.0" name="param_algorithm_thresholds_peak_bound" optional="True" type="float" value="10.0"/> <param help="(-peak_bound_ms2_level) " label="Minimal peak intensity for MS/MS peaks" min="0.0" name="param_algorithm_thresholds_peak_bound_ms2_level" optional="True" type="float" value="10.0"/> <param help="(-correlation) If a peak has a lower correlation it is skipped" label="minimal correlation of a peak and the raw signal" max="1.0" min="0.0" name="param_algorithm_thresholds_correlation" optional="True" type="float" value="0.5"/> <param help="(-noise_level) " label="noise level for the search of the peak endpoints" min="0.0" name="param_algorithm_thresholds_noise_level" optional="True" type="float" value="0.1"/> <param help="(-search_radius) " label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" min="0" name="param_algorithm_thresholds_search_radius" optional="True" type="integer" value="3"/> <param help="(-spacing) Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most" label="Spacing of the CWT" min="0.0" name="param_algorithm_wavelet_transform_spacing" optional="True" type="float" value="0.001"/> <param checked="false" falsevalue="" help="(-deconvolution) " label="If you want heavily overlapping peaks to be separated set this value to "true"" name="param_algorithm_deconvolution_deconvolution" optional="True" truevalue="-algorithm:deconvolution:deconvolution" type="boolean"/> <param help="(-asym_threshold) " label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" min="0.0" name="param_algorithm_deconvolution_asym_threshold" optional="True" type="float" value="0.3"/> <param help="(-left_width) " label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" min="0.0" name="param_algorithm_deconvolution_left_width" optional="True" type="float" value="2.0"/> <param help="(-right_width) " label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" min="0.0" name="param_algorithm_deconvolution_right_width" optional="True" type="float" value="2.0"/> <param help="(-scaling) The initial value is used for charge 1, for higher charges it is adapted to scaling/charge" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" min="0.0" name="param_algorithm_deconvolution_scaling" optional="True" type="float" value="0.12"/> <param help="(-fwhm_threshold) " label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" min="0.0" name="param_algorithm_deconvolution_fitting_fwhm_threshold" optional="True" type="float" value="0.7"/> <param help="(-eps_abs) " label="if the absolute error gets smaller than this value the fitting is stopped" min="0.0" name="param_algorithm_deconvolution_fitting_eps_abs" optional="True" type="float" value="9.99999974738e-06"/> <param help="(-eps_rel) " label="if the relative error gets smaller than this value the fitting is stopped" min="0.0" name="param_algorithm_deconvolution_fitting_eps_rel" optional="True" type="float" value="9.99999974738e-06"/> <param help="(-max_iteration) " label="maximal number of iterations for the fitting step" min="1" name="param_algorithm_deconvolution_fitting_max_iteration" optional="True" type="integer" value="10"/> <param help="(-position) " label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" min="0.0" name="param_algorithm_deconvolution_fitting_penalties_position" optional="True" type="float" value="0.0"/> <param help="(-height) " label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" min="0.0" name="param_algorithm_deconvolution_fitting_penalties_height" optional="True" type="float" value="1.0"/> <param help="(-left_width) " label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" min="0.0" name="param_algorithm_deconvolution_fitting_penalties_left_width" optional="True" type="float" value="0.0"/> <param help="(-right_width) " label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" min="0.0" name="param_algorithm_deconvolution_fitting_penalties_right_width" optional="True" type="float" value="0.0"/> <param help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)" label="maximal intensity considered for histogram construction" min="-1" name="param_algorithm_SignalToNoiseEstimationParameter_max_intensity" optional="True" type="integer" value="-1"/> <param help="(-auto_max_stdev_factor) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" max="999.0" min="0.0" name="param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor" optional="True" type="float" value="3.0"/> <param help="(-auto_max_percentile) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" max="100" min="0" name="param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile" optional="True" type="integer" value="95"/> <param help="(-auto_mode) " label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" max="1" min="-1" name="param_algorithm_SignalToNoiseEstimationParameter_auto_mode" optional="True" type="integer" value="0"/> <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_SignalToNoiseEstimationParameter_win_len" optional="True" type="float" value="200.0"/> <param help="(-bin_count) " label="number of bins for intensity values" min="3" name="param_algorithm_SignalToNoiseEstimationParameter_bin_count" optional="True" type="integer" value="30"/> <param help="(-stdev_mp) " label="multiplier for stdev" max="999.0" min="0.01" name="param_algorithm_SignalToNoiseEstimationParameter_stdev_mp" optional="True" type="float" value="3.0"/> <param help="(-min_required_elements) " label="minimum number of elements required in a window (otherwise it is considered sparse)" min="1" name="param_algorithm_SignalToNoiseEstimationParameter_min_required_elements" optional="True" type="integer" value="10"/> <param help="(-noise_for_empty_window) " label="noise value used for sparse windows" name="param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20"/> </expand> </inputs> <outputs> <data format="mzml" name="param_out"/> </outputs> <help>Finds mass spectrometric peaks in profile mass spectra. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html</help> </tool>