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comparison TOFCalibration.xml @ 9:40a101cabd0e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:59:26 +0000
parents 0d91d2be68be
children 90f459a4da0e
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8:2b75abf1a2c5 9:40a101cabd0e
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="TOFCalibration" name="TOFCalibration" version="2.3.0"> 4 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Applies time of flight calibration.</description> 5 <description>Applies time of flight calibration.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">TOFCalibration</token> 7 <token name="@EXECUTABLE@">TOFCalibration</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[TOFCalibration 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 $param_out 22 mkdir ext_calibrants &&
20 #end if 23 ln -s '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' &&
21 #if $param_ext_calibrants: 24 mkdir ref_masses &&
22 -ext_calibrants $param_ext_calibrants 25 ln -s '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' &&
23 #end if 26 mkdir tof_const &&
24 #if $param_ref_masses: 27 ln -s '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' &&
25 -ref_masses $param_ref_masses 28
26 #end if 29 ## Main program call
27 #if $param_tof_const: 30
28 -tof_const $param_tof_const 31 set -o pipefail &&
29 #end if 32 @EXECUTABLE@ -write_ctd ./ &&
30 #if $param_peak_data: 33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
31 -peak_data 34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
32 #end if 35 -in
33 #if $param_algorithm_PeakPicker_signal_to_noise: 36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
34 -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise 37 -out
35 #end if 38 'out/output.${gxy2omsext("mzml")}'
36 #if $param_algorithm_PeakPicker_peak_width: 39 -ext_calibrants
37 -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width 40 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)'
38 #end if 41 -ref_masses
39 #if $param_algorithm_PeakPicker_estimate_peak_width: 42 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)'
40 -algorithm:PeakPicker:estimate_peak_width 43 -tof_const
41 #end if 44 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)'
42 #if $adv_opts.adv_opts_selector=='advanced': 45
43 #if $adv_opts.param_force: 46 ## Postprocessing
44 -force 47 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
45 #end if 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
46 #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage: 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
47 -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage 50 #end if]]></command>
48 #end if 51 <configfiles>
49 #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor: 52 <inputs name="args_json" data_style="paths"/>
50 -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
51 #end if 54 </configfiles>
52 #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor:
53 -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor
54 #end if
55 #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations:
56 -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations
57 #end if
58 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position:
59 -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position
60 #end if
61 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width:
62 -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width
63 #end if
64 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width:
65 -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width
66 #end if
67 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height:
68 -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height
69 #end if
70 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz:
71 -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz
72 #end if
73 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance:
74 -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance
75 #end if
76 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound:
77 -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound
78 #end if
79 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level:
80 -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level
81 #end if
82 #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation:
83 -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation
84 #end if
85 #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level:
86 -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level
87 #end if
88 #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius:
89 -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius
90 #end if
91 #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing:
92 -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing
93 #end if
94 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution:
95 -algorithm:PeakPicker:deconvolution:deconvolution
96 #end if
97 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold:
98 -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold
99 #end if
100 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width:
101 -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width
102 #end if
103 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width:
104 -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width
105 #end if
106 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling:
107 -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling
108 #end if
109 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold:
110 -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold
111 #end if
112 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs:
113 -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs
114 #end if
115 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel:
116 -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel
117 #end if
118 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration:
119 -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration
120 #end if
121 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position:
122 -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position
123 #end if
124 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height:
125 -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height
126 #end if
127 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width:
128 -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width
129 #end if
130 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width:
131 -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width
132 #end if
133 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity:
134 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity
135 #end if
136 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor:
137 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor
138 #end if
139 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile:
140 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile
141 #end if
142 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode:
143 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode
144 #end if
145 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len:
146 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len
147 #end if
148 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count:
149 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count
150 #end if
151 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp:
152 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp
153 #end if
154 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements:
155 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements
156 #end if
157 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window:
158 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window
159 #end if
160 #end if
161 ]]></command>
162 <inputs> 55 <inputs>
163 <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/> 56 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/>
164 <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/> 57 <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
165 <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) "/> 58 <param name="ref_masses" argument="-ref_masses" type="data" format="txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select txt data sets(s)"/>
166 <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants &lt;br&gt;per set, depending on the conversion type. Either one set for all calibrant spectra &lt;br&gt;(tab separated), or one for each spectrum. &lt;br&gt;For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/> 59 <param name="tof_const" argument="-tof_const" type="data" format="csv" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select csv data sets(s)"/>
167 <param name="param_peak_data" display="radio" type="boolean" truevalue="-peak_data" falsevalue="" 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) "/> 60 <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/>
168 <param name="param_algorithm_PeakPicker_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) "/> 61 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
169 <param name="param_algorithm_PeakPicker_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/> 62 <section name="PeakPicker" title="" help="" expanded="false">
170 <param name="param_algorithm_PeakPicker_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:PeakPicker: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"/> 63 <param name="signal_to_noise" argument="-algorithm:PeakPicker: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=""/>
171 <expand macro="advanced_options"> 64 <param name="centroid_percentage" argument="-algorithm:PeakPicker: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"/>
172 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 65 <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
173 <param name="param_algorithm_PeakPicker_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"/> 66 <param name="estimate_peak_width" argument="-algorithm:PeakPicker: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"/>
174 <param name="param_algorithm_PeakPicker_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"/> 67 <param name="fwhm_lower_bound_factor" argument="-algorithm:PeakPicker: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"/>
175 <param name="param_algorithm_PeakPicker_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"/> 68 <param name="fwhm_upper_bound_factor" argument="-algorithm:PeakPicker: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"/>
176 <param name="param_algorithm_PeakPicker_optimization_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations) "/> 69 <section name="optimization" title="" help="" expanded="false">
177 <param name="param_algorithm_PeakPicker_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) "/> 70 <param name="iterations" argument="-algorithm:PeakPicker:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
178 <param name="param_algorithm_PeakPicker_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) "/> 71 <section name="penalties" title="" help="" expanded="false">
179 <param name="param_algorithm_PeakPicker_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) "/> 72 <param name="position" argument="-algorithm:PeakPicker: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=""/>
180 <param name="param_algorithm_PeakPicker_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) "/> 73 <param name="left_width" argument="-algorithm:PeakPicker: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=""/>
181 <param name="param_algorithm_PeakPicker_optimization_2d_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz) "/> 74 <param name="right_width" argument="-algorithm:PeakPicker: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=""/>
182 <param name="param_algorithm_PeakPicker_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) "/> 75 <param name="height" argument="-algorithm:PeakPicker: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=""/>
183 <param name="param_algorithm_PeakPicker_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/> 76 </section>
184 <param name="param_algorithm_PeakPicker_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) "/> 77 <section name="2d" title="" help="" expanded="false">
185 <param name="param_algorithm_PeakPicker_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"/> 78 <param name="tolerance_mz" argument="-algorithm:PeakPicker:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
186 <param name="param_algorithm_PeakPicker_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) "/> 79 <param name="max_peak_distance" argument="-algorithm:PeakPicker: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=""/>
187 <param name="param_algorithm_PeakPicker_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) "/> 80 </section>
188 <param name="param_algorithm_PeakPicker_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"/> 81 </section>
189 <param name="param_algorithm_PeakPicker_deconvolution_deconvolution" display="radio" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution" falsevalue="" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help="(-deconvolution) "/> 82 <section name="thresholds" title="" help="" expanded="false">
190 <param name="param_algorithm_PeakPicker_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) "/> 83 <param name="peak_bound" argument="-algorithm:PeakPicker:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
191 <param name="param_algorithm_PeakPicker_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) "/> 84 <param name="peak_bound_ms2_level" argument="-algorithm:PeakPicker:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
192 <param name="param_algorithm_PeakPicker_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) "/> 85 <param name="correlation" argument="-algorithm:PeakPicker: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"/>
193 <param name="param_algorithm_PeakPicker_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"/> 86 <param name="noise_level" argument="-algorithm:PeakPicker:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
194 <param name="param_algorithm_PeakPicker_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) "/> 87 <param name="search_radius" argument="-algorithm:PeakPicker: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=""/>
195 <param name="param_algorithm_PeakPicker_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) "/> 88 </section>
196 <param name="param_algorithm_PeakPicker_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) "/> 89 <section name="wavelet_transform" title="" help="" expanded="false">
197 <param name="param_algorithm_PeakPicker_deconvolution_fitting_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration) "/> 90 <param name="spacing" argument="-algorithm:PeakPicker: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"/>
198 <param name="param_algorithm_PeakPicker_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) "/> 91 </section>
199 <param name="param_algorithm_PeakPicker_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) "/> 92 <section name="deconvolution" title="" help="" expanded="false">
200 <param name="param_algorithm_PeakPicker_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) "/> 93 <param name="deconvolution" argument="-algorithm:PeakPicker:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help=""/>
201 <param name="param_algorithm_PeakPicker_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) "/> 94 <param name="asym_threshold" argument="-algorithm:PeakPicker: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=""/>
202 <param name="param_algorithm_PeakPicker_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)"/> 95 <param name="left_width" argument="-algorithm:PeakPicker: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=""/>
203 <param name="param_algorithm_PeakPicker_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) "/> 96 <param name="right_width" argument="-algorithm:PeakPicker: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=""/>
204 <param name="param_algorithm_PeakPicker_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) "/> 97 <param name="scaling" argument="-algorithm:PeakPicker: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"/>
205 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/> 98 <section name="fitting" title="" help="" expanded="false">
206 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> 99 <param name="fwhm_threshold" argument="-algorithm:PeakPicker: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=""/>
207 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> 100 <param name="eps_abs" argument="-algorithm:PeakPicker: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=""/>
208 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp) "/> 101 <param name="eps_rel" argument="-algorithm:PeakPicker: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=""/>
209 <param name="param_algorithm_PeakPicker_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) "/> 102 <param name="max_iteration" argument="-algorithm:PeakPicker:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
210 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> 103 <section name="penalties" title="" help="" expanded="false">
104 <param name="position" argument="-algorithm:PeakPicker: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=""/>
105 <param name="height" argument="-algorithm:PeakPicker: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=""/>
106 <param name="left_width" argument="-algorithm:PeakPicker: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=""/>
107 <param name="right_width" argument="-algorithm:PeakPicker: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=""/>
108 </section>
109 </section>
110 </section>
111 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
112 <param name="max_intensity" argument="-algorithm:PeakPicker: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)"/>
113 <param name="auto_max_stdev_factor" argument="-algorithm:PeakPicker: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=""/>
114 <param name="auto_max_percentile" argument="-algorithm:PeakPicker: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=""/>
115 <param name="auto_mode" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" min="-1" max="1" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help=""/>
116 <param name="win_len" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
117 <param name="bin_count" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
118 <param name="stdev_mp" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
119 <param name="min_required_elements" argument="-algorithm:PeakPicker: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=""/>
120 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
121 </section>
122 </section>
123 </section>
124 <expand macro="adv_opts_macro">
125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
127 <expand macro="list_string_san"/>
128 </param>
211 </expand> 129 </expand>
130 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
132 </param>
212 </inputs> 133 </inputs>
213 <outputs> 134 <outputs>
214 <data name="param_out" format="mzml"/> 135 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
138 </data>
215 </outputs> 139 </outputs>
216 <help>Applies time of flight calibration. 140 <tests>
141 <expand macro="autotest_TOFCalibration"/>
142 <expand macro="manutest_TOFCalibration"/>
143 </tests>
144 <help><![CDATA[Applies time of flight calibration.
217 145
218 146
219 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_TOFCalibration.html</help> 147 For more information, visit http://www.openms.de/documentation/TOPP_TOFCalibration.html]]></help>
148 <expand macro="references"/>
220 </tool> 149 </tool>