Mercurial > repos > galaxyp > openms_peakpickerwavelet
comparison PeakPickerWavelet.xml @ 9:bf3353f27d33 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 19:40:42 +0000 |
parents | 17913dee7f88 |
children | 341af0b11af9 |
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8:fe0427887130 | 9:bf3353f27d33 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 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 CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> | 3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.3.0"> | 4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> | 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> | 7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[PeakPickerWavelet | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
17 #end if | 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
18 #if $param_out: | 21 mkdir out && |
19 -out $param_out | 22 |
20 #end if | 23 ## Main program call |
21 #if $param_algorithm_signal_to_noise: | 24 |
22 -algorithm:signal_to_noise $param_algorithm_signal_to_noise | 25 set -o pipefail && |
23 #end if | 26 @EXECUTABLE@ -write_ctd ./ && |
24 #if $param_algorithm_peak_width: | 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
25 -algorithm:peak_width $param_algorithm_peak_width | 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
26 #end if | 29 -in |
27 #if $param_algorithm_estimate_peak_width: | 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
28 -algorithm:estimate_peak_width | 31 -out |
29 #end if | 32 'out/output.${gxy2omsext("mzml")}' |
30 #if $adv_opts.adv_opts_selector=='advanced': | 33 |
31 #if $adv_opts.param_write_peak_meta_data: | 34 ## Postprocessing |
32 -write_peak_meta_data | 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
33 #end if | 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
34 #if $adv_opts.param_force: | 37 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
35 -force | 38 #end if]]></command> |
36 #end if | 39 <configfiles> |
37 #if $adv_opts.param_algorithm_centroid_percentage: | 40 <inputs name="args_json" data_style="paths"/> |
38 -algorithm:centroid_percentage $adv_opts.param_algorithm_centroid_percentage | 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
39 #end if | 42 </configfiles> |
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> | 43 <inputs> |
154 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> | 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> |
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) "/> | 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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) "/> | 46 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> |
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"/> | 47 <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" 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="If it is 1 the centroid position corresponds to the position of the highest intensity"/> |
158 <expand macro="advanced_options"> | 48 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> |
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!"/> | 49 <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/> |
160 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 50 <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" optional="true" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/> |
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"/> | 51 <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" optional="true" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/> |
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"/> | 52 <section name="optimization" title="" help="" expanded="false"> |
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"/> | 53 <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/> |
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) "/> | 54 <section name="penalties" title="" help="" expanded="false"> |
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) "/> | 55 <param name="position" argument="-algorithm:optimization:penalties:position" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 56 <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 57 <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 58 <param name="height" argument="-algorithm:optimization:penalties:height" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 59 </section> |
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) "/> | 60 <section name="2d" title="" help="" expanded="false"> |
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) "/> | 61 <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/> |
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) "/> | 62 <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/> |
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"/> | 63 </section> |
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) "/> | 64 </section> |
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) "/> | 65 <section name="thresholds" title="" help="" expanded="false"> |
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"/> | 66 <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/> |
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) "/> | 67 <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/> |
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) "/> | 68 <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/> |
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) "/> | 69 <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/> |
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) "/> | 70 <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" optional="true" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/> |
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"/> | 71 </section> |
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) "/> | 72 <section name="wavelet_transform" title="" help="" expanded="false"> |
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) "/> | 73 <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" optional="true" min="0.0" value="0.001" label="Spacing of the CWT" help="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"/> |
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) "/> | 74 </section> |
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) "/> | 75 <section name="deconvolution" title="" help="" expanded="false"> |
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) "/> | 76 <param name="deconvolution" argument="-algorithm:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to "true"" help=""/> |
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) "/> | 77 <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 78 <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" optional="true" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/> |
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) "/> | 79 <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" optional="true" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/> |
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)"/> | 80 <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" optional="true" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/> |
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) "/> | 81 <section name="fitting" title="" help="" expanded="false"> |
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) "/> | 82 <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 83 <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/> |
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) "/> | 84 <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/> |
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) "/> | 85 <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/> |
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) "/> | 86 <section name="penalties" title="" help="" expanded="false"> |
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) "/> | 87 <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" optional="true" min="0.0" 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=""/> |
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) "/> | 88 <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" optional="true" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/> |
89 <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" optional="true" min="0.0" 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=""/> | |
90 <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" optional="true" min="0.0" 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=""/> | |
91 </section> | |
92 </section> | |
93 </section> | |
94 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false"> | |
95 <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="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)"/> | |
96 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/> | |
97 <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/> | |
98 <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" min="-1" max="1" 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=""/> | |
99 <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/> | |
100 <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/> | |
101 <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/> | |
102 <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> | |
103 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> | |
104 </section> | |
105 </section> | |
106 <expand macro="adv_opts_macro"> | |
107 <param name="write_peak_meta_data" argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/> | |
108 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
109 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
110 <expand macro="list_string_san"/> | |
111 </param> | |
199 </expand> | 112 </expand> |
113 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
114 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
115 </param> | |
200 </inputs> | 116 </inputs> |
201 <outputs> | 117 <outputs> |
202 <data name="param_out" format="mzml"/> | 118 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
121 </data> | |
203 </outputs> | 122 </outputs> |
204 <help>Finds mass spectrometric peaks in profile mass spectra. | 123 <tests> |
124 <expand macro="autotest_PeakPickerWavelet"/> | |
125 <expand macro="manutest_PeakPickerWavelet"/> | |
126 </tests> | |
127 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. | |
205 | 128 |
206 | 129 |
207 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeakPickerWavelet.html</help> | 130 For more information, visit http://www.openms.de/documentation/TOPP_PeakPickerWavelet.html]]></help> |
131 <expand macro="references"/> | |
208 </tool> | 132 </tool> |