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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:42:11 +0000
parents 9f0e189d093c
children
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13:9f0e189d093c 14:b6f7cec6cc9e
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Mass Correction and Calibration]-->
4 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies time of flight calibration.</description> 4 <description>Applies time of flight calibration</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">TOFCalibration</token> 6 <token name="@EXECUTABLE@">TOFCalibration</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 mkdir ext_calibrants && 19 mkdir ext_calibrants &&
21 ln -s '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' && 20 cp '$ext_calibrants' 'ext_calibrants/${re.sub("[^\w\-_]", "_", $ext_calibrants.element_identifier)}.$gxy2omsext($ext_calibrants.ext)' &&
22 mkdir ref_masses && 21 mkdir ref_masses &&
23 ln -s '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' && 22 cp '$ref_masses' 'ref_masses/${re.sub("[^\w\-_]", "_", $ref_masses.element_identifier)}.$gxy2omsext($ref_masses.ext)' &&
24 mkdir tof_const && 23 mkdir tof_const &&
25 ln -s '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' && 24 cp '$tof_const' 'tof_const/${re.sub("[^\w\-_]", "_", $tof_const.element_identifier)}.$gxy2omsext($tof_const.ext)' &&
26 25
27 ## Main program call 26 ## Main program call
28 27
29 set -o pipefail && 28 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ && 29 @EXECUTABLE@ -write_ctd ./ &&
49 <configfiles> 48 <configfiles>
50 <inputs name="args_json" data_style="paths"/> 49 <inputs name="args_json" data_style="paths"/>
51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 50 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
52 </configfiles> 51 </configfiles>
53 <inputs> 52 <inputs>
54 <param argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> 53 <param argument="-in" type="data" format="mzml" label="input peak or raw data file" help=" select mzml data sets(s)"/>
55 <param 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)"/> 54 <param argument="-ext_calibrants" type="data" format="mzml" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
56 <param argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/> 55 <param argument="-ref_masses" type="data" format="tabular,txt" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
57 <param argument="-tof_const" type="data" format="tabular" 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 tabular data sets(s)"/> 56 <param argument="-tof_const" type="data" format="tabular" 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 tabular data sets(s)"/>
58 <param 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=""/> 57 <param 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=""/>
59 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> 58 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
60 <section name="PeakPicker" title="" help="" expanded="false"> 59 <section name="PeakPicker" title="" help="" expanded="false">
61 <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=""/> 60 <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
62 <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"/> 61 <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" 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"/>
63 <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=""/> 62 <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
64 <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"/> 63 <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"/>
65 <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"/> 64 <param name="fwhm_lower_bound_factor" argument="-algorithm:PeakPicker:fwhm_lower_bound_factor" type="float" 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"/>
66 <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"/> 65 <param name="fwhm_upper_bound_factor" argument="-algorithm:PeakPicker:fwhm_upper_bound_factor" type="float" 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"/>
67 <section name="optimization" title="" help="" expanded="false"> 66 <section name="optimization" title="" help="" expanded="false">
68 <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=""/> 67 <param name="iterations" argument="-algorithm:PeakPicker:optimization:iterations" type="integer" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
69 <section name="penalties" title="" help="" expanded="false"> 68 <section name="penalties" title="" help="" expanded="false">
70 <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=""/> 69 <param name="position" argument="-algorithm:PeakPicker:optimization:penalties:position" type="float" 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=""/>
71 <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=""/> 70 <param name="left_width" argument="-algorithm:PeakPicker:optimization:penalties:left_width" type="float" 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=""/>
72 <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=""/> 71 <param name="right_width" argument="-algorithm:PeakPicker:optimization:penalties:right_width" type="float" 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=""/>
73 <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=""/> 72 <param name="height" argument="-algorithm:PeakPicker:optimization:penalties:height" type="float" 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=""/>
74 </section> 73 </section>
75 <section name="2d" title="" help="" expanded="false"> 74 <section name="2d" title="" help="" expanded="false">
76 <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=""/> 75 <param name="tolerance_mz" argument="-algorithm:PeakPicker:optimization:2d:tolerance_mz" type="float" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
77 <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=""/> 76 <param name="max_peak_distance" argument="-algorithm:PeakPicker:optimization:2d:max_peak_distance" type="float" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
78 </section> 77 </section>
79 </section> 78 </section>
80 <section name="thresholds" title="" help="" expanded="false"> 79 <section name="thresholds" title="" help="" expanded="false">
81 <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=""/> 80 <param name="peak_bound" argument="-algorithm:PeakPicker:thresholds:peak_bound" type="float" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
82 <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=""/> 81 <param name="peak_bound_ms2_level" argument="-algorithm:PeakPicker:thresholds:peak_bound_ms2_level" type="float" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
83 <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"/> 82 <param name="correlation" argument="-algorithm:PeakPicker:thresholds:correlation" type="float" 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"/>
84 <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=""/> 83 <param name="noise_level" argument="-algorithm:PeakPicker:thresholds:noise_level" type="float" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
85 <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=""/> 84 <param name="search_radius" argument="-algorithm:PeakPicker:thresholds:search_radius" type="integer" 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=""/>
86 </section> 85 </section>
87 <section name="wavelet_transform" title="" help="" expanded="false"> 86 <section name="wavelet_transform" title="" help="" expanded="false">
88 <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"/> 87 <param name="spacing" argument="-algorithm:PeakPicker:wavelet_transform:spacing" type="float" 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"/>
89 </section> 88 </section>
90 <section name="deconvolution" title="" help="" expanded="false"> 89 <section name="deconvolution" title="" help="" expanded="false">
91 <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=""/> 90 <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=""/>
92 <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=""/> 91 <param name="asym_threshold" argument="-algorithm:PeakPicker:deconvolution:asym_threshold" type="float" 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=""/>
93 <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=""/> 92 <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:left_width" type="float" 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=""/>
94 <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=""/> 93 <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:right_width" type="float" 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=""/>
95 <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"/> 94 <param name="scaling" argument="-algorithm:PeakPicker:deconvolution:scaling" type="float" 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"/>
96 <section name="fitting" title="" help="" expanded="false"> 95 <section name="fitting" title="" help="" expanded="false">
97 <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=""/> 96 <param name="fwhm_threshold" argument="-algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold" type="float" 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=""/>
98 <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=""/> 97 <param name="eps_abs" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_abs" type="float" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
99 <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=""/> 98 <param name="eps_rel" argument="-algorithm:PeakPicker:deconvolution:fitting:eps_rel" type="float" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
100 <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=""/> 99 <param name="max_iteration" argument="-algorithm:PeakPicker:deconvolution:fitting:max_iteration" type="integer" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
101 <section name="penalties" title="" help="" expanded="false"> 100 <section name="penalties" title="" help="" expanded="false">
102 <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=""/> 101 <param name="position" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:position" type="float" 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=""/>
103 <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=""/> 102 <param name="height" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:height" type="float" 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=""/>
104 <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=""/> 103 <param name="left_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:left_width" type="float" 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=""/>
105 <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=""/> 104 <param name="right_width" argument="-algorithm:PeakPicker:deconvolution:fitting:penalties:right_width" type="float" 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=""/>
106 </section> 105 </section>
107 </section> 106 </section>
108 </section> 107 </section>
109 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false"> 108 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
110 <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)"/> 109 <param name="max_intensity" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity" type="integer" 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)"/>
111 <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=""/> 110 <param name="auto_max_stdev_factor" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" 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=""/>
112 <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=""/> 111 <param name="auto_max_percentile" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
113 <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=""/> 112 <param name="auto_mode" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode" type="integer" 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=""/>
114 <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=""/> 113 <param name="win_len" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
115 <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=""/> 114 <param name="bin_count" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
116 <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=""/> 115 <param name="stdev_mp" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp" type="float" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
117 <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=""/> 116 <param name="min_required_elements" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
118 <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=""/> 117 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
119 </section> 118 </section>
120 </section> 119 </section>
121 </section> 120 </section>
122 <expand macro="adv_opts_macro"> 121 <expand macro="adv_opts_macro">
123 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
124 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 123 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
125 <expand macro="list_string_san" name="test"/> 124 <expand macro="list_string_san" name="test"/>
126 </param> 125 </param>
127 </expand> 126 </expand>
128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
129 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
133 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 132 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
134 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
135 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
136 </data> 135 </data>
137 </outputs> 136 </outputs>
138 <tests><!-- TOPP_TOFCalibration_1 --> 137 <tests>
138 <!-- TOPP_TOFCalibration_1 -->
139 <test expect_num_outputs="2"> 139 <test expect_num_outputs="2">
140 <section name="adv_opts"> 140 <section name="adv_opts">
141 <param name="force" value="false"/> 141 <param name="force" value="false"/>
142 <param name="test" value="true"/> 142 <param name="test" value="true"/>
143 </section> 143 </section>
144 <param name="in" value="TOFCalibration_1_input.mzML"/> 144 <param name="in" value="TOFCalibration_1_input.mzML"/>
145 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 145 <output name="out" value="TOFCalibration.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
146 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> 146 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
147 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> 147 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
148 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> 148 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
149 <param name="peak_data" value="false"/> 149 <param name="peak_data" value="false"/>
150 <section name="algorithm"> 150 <section name="algorithm">
214 <output name="ctd_out" ftype="xml"> 214 <output name="ctd_out" ftype="xml">
215 <assert_contents> 215 <assert_contents>
216 <is_valid_xml/> 216 <is_valid_xml/>
217 </assert_contents> 217 </assert_contents>
218 </output> 218 </output>
219 <assert_stdout>
220 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
221 </assert_stdout>
219 </test> 222 </test>
220 <!-- TOPP_TOFCalibration_2 --> 223 <!-- TOPP_TOFCalibration_2 -->
221 <test expect_num_outputs="2"> 224 <test expect_num_outputs="2">
222 <section name="adv_opts"> 225 <section name="adv_opts">
223 <param name="force" value="false"/> 226 <param name="force" value="false"/>
224 <param name="test" value="true"/> 227 <param name="test" value="true"/>
225 </section> 228 </section>
226 <param name="in" value="TOFCalibration_2_input.mzML"/> 229 <param name="in" value="TOFCalibration_2_input.mzML"/>
227 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 230 <output name="out" value="TOFCalibration_2.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
228 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> 231 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
229 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> 232 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
230 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> 233 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
231 <param name="peak_data" value="true"/> 234 <param name="peak_data" value="true"/>
232 <section name="algorithm"> 235 <section name="algorithm">
296 <output name="ctd_out" ftype="xml"> 299 <output name="ctd_out" ftype="xml">
297 <assert_contents> 300 <assert_contents>
298 <is_valid_xml/> 301 <is_valid_xml/>
299 </assert_contents> 302 </assert_contents>
300 </output> 303 </output>
304 <assert_stdout>
305 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
306 </assert_stdout>
301 </test> 307 </test>
302 </tests> 308 </tests>
303 <help><![CDATA[Applies time of flight calibration. 309 <help><![CDATA[Applies time of flight calibration.
304 310
305 311
306 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TOFCalibration.html]]></help> 312 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TOFCalibration.html]]></help>
307 <expand macro="references"/> 313 <expand macro="references"/>
308 </tool> 314 </tool>