Mercurial > repos > bgruening > openms
diff TOFCalibration.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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--- a/TOFCalibration.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/TOFCalibration.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,125 +1,221 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="TOFCalibration" name="TOFCalibration" version="1.12.0"> - <description>Applies time of flight calibration.</description> - <macros> - <token name="@EXECUTABLE@">TOFCalibration</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>TOFCalibration +<?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="TOFCalibration" name="TOFCalibration" version="2.0.0"> + <description>Applies time of flight calibration.</description> + <macros> + <token name="@EXECUTABLE@">TOFCalibration</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>TOFCalibration --in ${param_in} --out ${param_out} --ext_calibrants ${param_ext_calibrants} --ref_masses ${param_ref_masses} --tof_const ${param_tof_const} -${param_peak_data} --threads \${GALAXY_SLOTS:-24} --algorithm:PeakPicker:signal_to_noise ${param_signal_to_noise} --algorithm:PeakPicker:peak_width ${param_peak_width} -${param_estimate_peak_width} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_ext_calibrants: + -ext_calibrants $param_ext_calibrants +#end if +#if $param_ref_masses: + -ref_masses $param_ref_masses +#end if +#if $param_tof_const: + -tof_const $param_tof_const +#end if +#if $param_peak_data: + -peak_data +#end if +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_PeakPicker_signal_to_noise: + -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise +#end if +#if $param_algorithm_PeakPicker_peak_width: + -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width +#end if +#if $param_algorithm_PeakPicker_estimate_peak_width: + -algorithm:PeakPicker:estimate_peak_width +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:PeakPicker:centroid_percentage ${adv_opts.param_centroid_percentage} - -algorithm:PeakPicker:fwhm_lower_bound_factor ${adv_opts.param_fwhm_lower_bound_factor} - -algorithm:PeakPicker:fwhm_upper_bound_factor ${adv_opts.param_fwhm_upper_bound_factor} - -algorithm:PeakPicker:optimization:iterations ${adv_opts.param_iterations} - -algorithm:PeakPicker:optimization:penalties:position ${adv_opts.param_position} - -algorithm:PeakPicker:optimization:penalties:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:optimization:penalties:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:optimization:penalties:height ${adv_opts.param_height} - -algorithm:PeakPicker:optimization:2d:tolerance_mz ${adv_opts.param_tolerance_mz} - -algorithm:PeakPicker:optimization:2d:max_peak_distance ${adv_opts.param_max_peak_distance} - -algorithm:PeakPicker:thresholds:peak_bound ${adv_opts.param_peak_bound} - -algorithm:PeakPicker:thresholds:peak_bound_ms2_level ${adv_opts.param_peak_bound_ms2_level} - -algorithm:PeakPicker:thresholds:correlation ${adv_opts.param_correlation} - -algorithm:PeakPicker:thresholds:noise_level ${adv_opts.param_noise_level} - -algorithm:PeakPicker:thresholds:search_radius ${adv_opts.param_search_radius} - -algorithm:PeakPicker:wavelet_transform:spacing ${adv_opts.param_spacing} - ${adv_opts.param_deconvolution} - -algorithm:PeakPicker:deconvolution:asym_threshold ${adv_opts.param_asym_threshold} - -algorithm:PeakPicker:deconvolution:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:deconvolution:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:deconvolution:scaling ${adv_opts.param_scaling} - -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold ${adv_opts.param_fwhm_threshold} - -algorithm:PeakPicker:deconvolution:fitting:eps_abs ${adv_opts.param_eps_abs} - -algorithm:PeakPicker:deconvolution:fitting:eps_rel ${adv_opts.param_eps_rel} - -algorithm:PeakPicker:deconvolution:fitting:max_iteration ${adv_opts.param_max_iteration} - -algorithm:PeakPicker:deconvolution:fitting:penalties:position ${adv_opts.param_position} - -algorithm:PeakPicker:deconvolution:fitting:penalties:height ${adv_opts.param_height} - -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width ${adv_opts.param_left_width} - -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width ${adv_opts.param_right_width} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity ${adv_opts.param_max_intensity} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode ${adv_opts.param_auto_mode} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len ${adv_opts.param_win_len} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count ${adv_opts.param_bin_count} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp ${adv_opts.param_stdev_mp} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements ${adv_opts.param_min_required_elements} - -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage: + -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor: + -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor: + -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations: + -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position: + -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width: + -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width: + -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height: + -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz: + -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance: + -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound: + -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level: + -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation: + -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level: + -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius: + -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius +#end if + #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing: + -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution: + -algorithm:PeakPicker:deconvolution:deconvolution +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold: + -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width: + -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width: + -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling: + -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold: + -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs: + -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel: + -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration: + -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position: + -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height: + -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window +#end if #end if </command> - <inputs> - <param name="param_in" type="data" format="mzML" optional="False" label="input peak or raw data file " help="(-in)"/> - <param name="param_ext_calibrants" type="data" format="mzML" optional="False" label="input file containing the external calibrant spectra (peak or raw data)#br#" help="(-ext_calibrants)"/> - <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses)"/> - <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants. These can be either two or three constants#br#per set, depending on the conversion type. Either one set for all calibrant spectra #br#(tab separated), or one for each spectrum.#br#For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)" help="(-tof_const)"/> - <param name="param_peak_data" type="boolean" truevalue="-peak_data true" falsevalue="-peak_data false" checked="false" optional="True" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)." help="(-peak_data)"/> - <param name="param_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked." help="(-signal_to_noise)"/> - <param name="param_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks." help="(-peak_width)"/> - <param name="param_estimate_peak_width" type="boolean" truevalue="-algorithm:PeakPicker:estimate_peak_width true" falsevalue="-algorithm:PeakPicker:estimate_peak_width false" checked="false" optional="True" label="Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored." help="(-estimate_peak_width)"/> - <expand macro="advanced_options"> - <param name="param_centroid_percentage" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity." help="(-centroid_percentage)"/> - <param name="param_fwhm_lower_bound_factor" type="float" min="0.0" optional="True" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded." help="(-fwhm_lower_bound_factor)"/> - <param name="param_fwhm_upper_bound_factor" type="float" min="0.0" optional="True" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded." help="(-fwhm_upper_bound_factor)"/> - <param name="param_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations)"/> - <param name="param_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " help="(-position)"/> - <param name="param_left_width" type="float" min="0.0" optional="True" value="1.0" 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." help="(-left_width)"/> - <param name="param_right_width" type="float" min="0.0" optional="True" value="1.0" 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." help="(-right_width)"/> - <param name="param_height" type="float" min="0.0" optional="True" value="1.0" 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." help="(-height)"/> - <param name="param_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz)"/> - <param name="param_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluster" help="(-max_peak_distance)"/> - <param name="param_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity." help="(-peak_bound)"/> - <param name="param_peak_bound_ms2_level" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity for MS/MS peaks." help="(-peak_bound_ms2_level)"/> - <param name="param_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." help="(-correlation)"/> - <param name="param_noise_level" type="float" min="0.0" optional="True" value="0.1" label="noise level for the search of the peak endpoints." help="(-noise_level)"/> - <param name="param_search_radius" type="integer" min="0" optional="True" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help="(-search_radius)"/> - <param name="param_spacing" type="float" min="0.0" optional="True" value="0.001" label="spacing of the cwt." help="(-spacing)"/> - <param name="param_deconvolution" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution true" falsevalue="-algorithm:PeakPicker:deconvolution:deconvolution false" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to "true"" help="(-deconvolution)"/> - <param name="param_asym_threshold" type="float" min="0.0" optional="True" value="0.3" 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." help="(-asym_threshold)"/> - <param name="param_left_width" type="float" min="0.0" optional="True" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." help="(-left_width)"/> - <param name="param_right_width" type="float" min="0.0" optional="True" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." help="(-right_width)"/> - <param name="param_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge." help="(-scaling)"/> - <param name="param_fwhm_threshold" type="float" min="0.0" optional="True" value="0.7" 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." help="(-fwhm_threshold)"/> - <param name="param_eps_abs" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the absolute error gets smaller than this value the fitting is stopped." help="(-eps_abs)"/> - <param name="param_eps_rel" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the relative error gets smaller than this value the fitting is stopped." help="(-eps_rel)"/> - <param name="param_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration)"/> - <param name="param_position" type="float" min="0.0" optional="True" value="0.0" 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." help="(-position)"/> - <param name="param_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." help="(-height)"/> - <param name="param_left_width" type="float" min="0.0" optional="True" value="0.0" 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." help="(-left_width)"/> - <param name="param_right_width" type="float" min="0.0" optional="True" value="0.0" 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." help="(-right_width)"/> - <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. 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)." help="(-max_intensity)"/> - <param name="param_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor)"/> - <param name="param_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile)"/> - <param name="param_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode)"/> - <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/> - <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/> - <param name="param_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp)"/> - <param name="param_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements)"/> - <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="output file " format="mzML"/> - </outputs> - <help>**What it does** - -Applies time of flight calibration. + <inputs> + <param format="mzml" help="(-in) " label="input peak or raw data file" name="param_in" optional="False" type="data"/> + <param format="mzml" help="(-ext_calibrants) " label="input file containing the external calibrant spectra (peak or raw data)" name="param_ext_calibrants" optional="False" type="data"/> + <param format="txt" help="(-ref_masses) " label="input file containing reference masses of the external calibrant spectra (one per line)" name="param_ref_masses" optional="False" type="data"/> + <param format="tabular" help="(-tof_const) These can be either two or three constants <br>per set, depending on the conversion type. Either one set for all calibrant spectra <br>(tab separated), or one for each spectrum. <br>For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)" label="File containing TOF conversion constants" name="param_tof_const" optional="False" type="data"/> + <param checked="false" falsevalue="" help="(-peak_data) " label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" name="param_peak_data" optional="True" truevalue="-peak_data" type="boolean"/> + <param help="(-signal_to_noise) " label="Minimal signal to noise ratio for a peak to be picked" min="0.0" name="param_algorithm_PeakPicker_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_PeakPicker_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_PeakPicker_estimate_peak_width" optional="True" truevalue="-algorithm:PeakPicker:estimate_peak_width" type="boolean"/> + <expand macro="advanced_options"> + <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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_deconvolution_deconvolution" optional="True" truevalue="-algorithm:PeakPicker: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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_SignalToNoiseEstimationParameter_auto_mode" optional="True" type="integer" value="0"/> + <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_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_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20"/> + </expand> + </inputs> + <outputs> + <data format="mzml" name="param_out"/> + </outputs> + <help>Applies time of flight calibration. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html</help> + </tool>