Mercurial > repos > galaxyp > openms_peakpickerwavelet
comparison PeakPickerWavelet.xml @ 0:4ee66bd832d9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
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| date | Wed, 01 Mar 2017 12:27:41 -0500 |
| parents | |
| children | 22162ad90646 |
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| -1:000000000000 | 0:4ee66bd832d9 |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> | |
| 4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.1.0"> | |
| 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>PeakPickerWavelet | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 #if $param_algorithm_signal_to_noise: | |
| 22 -algorithm:signal_to_noise $param_algorithm_signal_to_noise | |
| 23 #end if | |
| 24 #if $param_algorithm_peak_width: | |
| 25 -algorithm:peak_width $param_algorithm_peak_width | |
| 26 #end if | |
| 27 #if $param_algorithm_estimate_peak_width: | |
| 28 -algorithm:estimate_peak_width | |
| 29 #end if | |
| 30 #if $adv_opts.adv_opts_selector=='advanced': | |
| 31 #if $adv_opts.param_write_peak_meta_data: | |
| 32 -write_peak_meta_data | |
| 33 #end if | |
| 34 #if $adv_opts.param_force: | |
| 35 -force | |
| 36 #end if | |
| 37 #if $adv_opts.param_algorithm_centroid_percentage: | |
| 38 -algorithm:centroid_percentage $adv_opts.param_algorithm_centroid_percentage | |
| 39 #end if | |
| 40 #if $adv_opts.param_algorithm_fwhm_lower_bound_factor: | |
| 41 -algorithm:fwhm_lower_bound_factor $adv_opts.param_algorithm_fwhm_lower_bound_factor | |
| 42 #end if | |
| 43 #if $adv_opts.param_algorithm_fwhm_upper_bound_factor: | |
| 44 -algorithm:fwhm_upper_bound_factor $adv_opts.param_algorithm_fwhm_upper_bound_factor | |
| 45 #end if | |
| 46 #if $adv_opts.param_algorithm_optimization_iterations: | |
| 47 -algorithm:optimization:iterations $adv_opts.param_algorithm_optimization_iterations | |
| 48 #end if | |
| 49 #if $adv_opts.param_algorithm_optimization_penalties_position: | |
| 50 -algorithm:optimization:penalties:position $adv_opts.param_algorithm_optimization_penalties_position | |
| 51 #end if | |
| 52 #if $adv_opts.param_algorithm_optimization_penalties_left_width: | |
| 53 -algorithm:optimization:penalties:left_width $adv_opts.param_algorithm_optimization_penalties_left_width | |
| 54 #end if | |
| 55 #if $adv_opts.param_algorithm_optimization_penalties_right_width: | |
| 56 -algorithm:optimization:penalties:right_width $adv_opts.param_algorithm_optimization_penalties_right_width | |
| 57 #end if | |
| 58 #if $adv_opts.param_algorithm_optimization_penalties_height: | |
| 59 -algorithm:optimization:penalties:height $adv_opts.param_algorithm_optimization_penalties_height | |
| 60 #end if | |
| 61 #if $adv_opts.param_algorithm_optimization_2d_tolerance_mz: | |
| 62 -algorithm:optimization:2d:tolerance_mz $adv_opts.param_algorithm_optimization_2d_tolerance_mz | |
| 63 #end if | |
| 64 #if $adv_opts.param_algorithm_optimization_2d_max_peak_distance: | |
| 65 -algorithm:optimization:2d:max_peak_distance $adv_opts.param_algorithm_optimization_2d_max_peak_distance | |
| 66 #end if | |
| 67 #if $adv_opts.param_algorithm_thresholds_peak_bound: | |
| 68 -algorithm:thresholds:peak_bound $adv_opts.param_algorithm_thresholds_peak_bound | |
| 69 #end if | |
| 70 #if $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level: | |
| 71 -algorithm:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level | |
| 72 #end if | |
| 73 #if $adv_opts.param_algorithm_thresholds_correlation: | |
| 74 -algorithm:thresholds:correlation $adv_opts.param_algorithm_thresholds_correlation | |
| 75 #end if | |
| 76 #if $adv_opts.param_algorithm_thresholds_noise_level: | |
| 77 -algorithm:thresholds:noise_level $adv_opts.param_algorithm_thresholds_noise_level | |
| 78 #end if | |
| 79 #if $adv_opts.param_algorithm_thresholds_search_radius: | |
| 80 -algorithm:thresholds:search_radius $adv_opts.param_algorithm_thresholds_search_radius | |
| 81 #end if | |
| 82 #if $adv_opts.param_algorithm_wavelet_transform_spacing: | |
| 83 -algorithm:wavelet_transform:spacing $adv_opts.param_algorithm_wavelet_transform_spacing | |
| 84 #end if | |
| 85 #if $adv_opts.param_algorithm_deconvolution_deconvolution: | |
| 86 -algorithm:deconvolution:deconvolution | |
| 87 #end if | |
| 88 #if $adv_opts.param_algorithm_deconvolution_asym_threshold: | |
| 89 -algorithm:deconvolution:asym_threshold $adv_opts.param_algorithm_deconvolution_asym_threshold | |
| 90 #end if | |
| 91 #if $adv_opts.param_algorithm_deconvolution_left_width: | |
| 92 -algorithm:deconvolution:left_width $adv_opts.param_algorithm_deconvolution_left_width | |
| 93 #end if | |
| 94 #if $adv_opts.param_algorithm_deconvolution_right_width: | |
| 95 -algorithm:deconvolution:right_width $adv_opts.param_algorithm_deconvolution_right_width | |
| 96 #end if | |
| 97 #if $adv_opts.param_algorithm_deconvolution_scaling: | |
| 98 -algorithm:deconvolution:scaling $adv_opts.param_algorithm_deconvolution_scaling | |
| 99 #end if | |
| 100 #if $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold: | |
| 101 -algorithm:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold | |
| 102 #end if | |
| 103 #if $adv_opts.param_algorithm_deconvolution_fitting_eps_abs: | |
| 104 -algorithm:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_deconvolution_fitting_eps_abs | |
| 105 #end if | |
| 106 #if $adv_opts.param_algorithm_deconvolution_fitting_eps_rel: | |
| 107 -algorithm:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_deconvolution_fitting_eps_rel | |
| 108 #end if | |
| 109 #if $adv_opts.param_algorithm_deconvolution_fitting_max_iteration: | |
| 110 -algorithm:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_deconvolution_fitting_max_iteration | |
| 111 #end if | |
| 112 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_position: | |
| 113 -algorithm:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_deconvolution_fitting_penalties_position | |
| 114 #end if | |
| 115 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_height: | |
| 116 -algorithm:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_deconvolution_fitting_penalties_height | |
| 117 #end if | |
| 118 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width: | |
| 119 -algorithm:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width | |
| 120 #end if | |
| 121 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width: | |
| 122 -algorithm:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width | |
| 123 #end if | |
| 124 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity: | |
| 125 -algorithm:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity | |
| 126 #end if | |
| 127 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor: | |
| 128 -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor | |
| 129 #end if | |
| 130 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile: | |
| 131 -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile | |
| 132 #end if | |
| 133 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode: | |
| 134 -algorithm:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode | |
| 135 #end if | |
| 136 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len: | |
| 137 -algorithm:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len | |
| 138 #end if | |
| 139 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count: | |
| 140 -algorithm:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count | |
| 141 #end if | |
| 142 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp: | |
| 143 -algorithm:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp | |
| 144 #end if | |
| 145 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements: | |
| 146 -algorithm:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements | |
| 147 #end if | |
| 148 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window: | |
| 149 -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window | |
| 150 #end if | |
| 151 #end if | |
| 152 </command> | |
| 153 <inputs> | |
| 154 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> | |
| 155 <param name="param_algorithm_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) "/> | |
| 156 <param name="param_algorithm_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/> | |
| 157 <param name="param_algorithm_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/> | |
| 158 <expand macro="advanced_options"> | |
| 159 <param name="param_write_peak_meta_data" display="radio" type="boolean" truevalue="-write_peak_meta_data" falsevalue="" checked="false" optional="True" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="(-write_peak_meta_data) Attention: this can blow up files, since seven arrays are stored per spectrum!"/> | |
| 160 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 161 <param name="param_algorithm_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" help="(-centroid_percentage) If it is 1 the centroid position corresponds to the position of the highest intensity"/> | |
| 162 <param name="param_algorithm_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" help="(-fwhm_lower_bound_factor) All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/> | |
| 163 <param name="param_algorithm_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" help="(-fwhm_upper_bound_factor) All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/> | |
| 164 <param name="param_algorithm_optimization_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations) "/> | |
| 165 <param name="param_algorithm_optimization_penalties_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) "/> | |
| 166 <param name="param_algorithm_optimization_penalties_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) "/> | |
| 167 <param name="param_algorithm_optimization_penalties_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) "/> | |
| 168 <param name="param_algorithm_optimization_penalties_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) "/> | |
| 169 <param name="param_algorithm_optimization_2d_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz) "/> | |
| 170 <param name="param_algorithm_optimization_2d_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluste" help="(-max_peak_distance) "/> | |
| 171 <param name="param_algorithm_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/> | |
| 172 <param name="param_algorithm_thresholds_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) "/> | |
| 173 <param name="param_algorithm_thresholds_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal" help="(-correlation) If a peak has a lower correlation it is skipped"/> | |
| 174 <param name="param_algorithm_thresholds_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) "/> | |
| 175 <param name="param_algorithm_thresholds_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) "/> | |
| 176 <param name="param_algorithm_wavelet_transform_spacing" type="float" min="0.0" optional="True" value="0.001" label="Spacing of the CWT" 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"/> | |
| 177 <param name="param_algorithm_deconvolution_deconvolution" display="radio" type="boolean" truevalue="-algorithm:deconvolution:deconvolution" falsevalue="" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to "true"" help="(-deconvolution) "/> | |
| 178 <param name="param_algorithm_deconvolution_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) "/> | |
| 179 <param name="param_algorithm_deconvolution_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) "/> | |
| 180 <param name="param_algorithm_deconvolution_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) "/> | |
| 181 <param name="param_algorithm_deconvolution_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="(-scaling) The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/> | |
| 182 <param name="param_algorithm_deconvolution_fitting_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) "/> | |
| 183 <param name="param_algorithm_deconvolution_fitting_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) "/> | |
| 184 <param name="param_algorithm_deconvolution_fitting_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) "/> | |
| 185 <param name="param_algorithm_deconvolution_fitting_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration) "/> | |
| 186 <param name="param_algorithm_deconvolution_fitting_penalties_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) "/> | |
| 187 <param name="param_algorithm_deconvolution_fitting_penalties_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) "/> | |
| 188 <param name="param_algorithm_deconvolution_fitting_penalties_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) "/> | |
| 189 <param name="param_algorithm_deconvolution_fitting_penalties_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) "/> | |
| 190 <param name="param_algorithm_SignalToNoiseEstimationParameter_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" 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)"/> | |
| 191 <param name="param_algorithm_SignalToNoiseEstimationParameter_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) "/> | |
| 192 <param name="param_algorithm_SignalToNoiseEstimationParameter_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) "/> | |
| 193 <param name="param_algorithm_SignalToNoiseEstimationParameter_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) "/> | |
| 194 <param name="param_algorithm_SignalToNoiseEstimationParameter_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> | |
| 195 <param name="param_algorithm_SignalToNoiseEstimationParameter_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> | |
| 196 <param name="param_algorithm_SignalToNoiseEstimationParameter_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp) "/> | |
| 197 <param name="param_algorithm_SignalToNoiseEstimationParameter_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) "/> | |
| 198 <param name="param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> | |
| 199 </expand> | |
| 200 </inputs> | |
| 201 <outputs> | |
| 202 <data name="param_out" format="mzml"/> | |
| 203 </outputs> | |
| 204 <help>Finds mass spectrometric peaks in profile mass spectra. | |
| 205 | |
| 206 | |
| 207 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html</help> | |
| 208 </tool> |