Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

comparison MRMTransitionGroupPicker.xml @ 13:78796b50831b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:11:36 +0000
parents a9000c129043
children 1c96645cbfbd
comparison
equal deleted inserted replaced
12:a93565208dba 13:78796b50831b
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Picks peaks in SRM/MRM chromatograms.</description> 5 <description>Picks peaks in SRM/MRM chromatograms.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token> 7 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
49 <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/> 47 <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
50 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 48 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
51 <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/> 49 <param name="stop_after_feature" argument="-algorithm:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
52 <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/> 50 <param name="stop_after_intensity_ratio" argument="-algorithm:stop_after_intensity_ratio" type="float" optional="true" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
53 <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/> 51 <param name="min_peak_width" argument="-algorithm:min_peak_width" type="float" optional="true" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
54 <param name="peak_integration" argument="-algorithm:peak_integration" display="radio" type="select" optional="false" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help=""> 52 <param name="peak_integration" argument="-algorithm:peak_integration" type="select" optional="true" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
55 <option value="original" selected="true">original</option> 53 <option value="original" selected="true">original</option>
56 <option value="smoothed">smoothed</option> 54 <option value="smoothed">smoothed</option>
57 <expand macro="list_string_san"/> 55 <expand macro="list_string_san" name="peak_integration"/>
58 </param> 56 </param>
59 <param name="background_subtraction" argument="-algorithm:background_subtraction" display="radio" type="select" optional="false" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation"> 57 <param name="background_subtraction" argument="-algorithm:background_subtraction" type="select" optional="true" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
60 <option value="none" selected="true">none</option> 58 <option value="none" selected="true">none</option>
61 <option value="original">original</option> 59 <option value="original">original</option>
62 <option value="exact">exact</option> 60 <option value="exact">exact</option>
63 <expand macro="list_string_san"/> 61 <expand macro="list_string_san" name="background_subtraction"/>
64 </param> 62 </param>
65 <param name="recalculate_peaks" argument="-algorithm:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/> 63 <param name="recalculate_peaks" argument="-algorithm:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
66 <param name="use_precursors" argument="-algorithm:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/> 64 <param name="use_precursors" argument="-algorithm:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
67 <param name="use_consensus" argument="-algorithm:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/> 65 <param name="use_consensus" argument="-algorithm:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
68 <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> 66 <param name="recalculate_peaks_max_z" argument="-algorithm:recalculate_peaks_max_z" type="float" optional="true" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
69 <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/> 67 <param name="minimal_quality" argument="-algorithm:minimal_quality" type="float" optional="true" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
70 <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/> 68 <param name="resample_boundary" argument="-algorithm:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
71 <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/> 69 <param name="compute_peak_quality" argument="-algorithm:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
72 <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/> 70 <param name="compute_peak_shape_metrics" argument="-algorithm:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
73 <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/> 71 <param name="compute_total_mi" argument="-algorithm:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
74 <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help=""> 72 <param name="boundary_selection_method" argument="-algorithm:boundary_selection_method" type="select" optional="true" label="Method to use when selecting the best boundaries for peaks" help="">
75 <option value="largest" selected="true">largest</option> 73 <option value="largest" selected="true">largest</option>
76 <option value="widest">widest</option> 74 <option value="widest">widest</option>
77 <expand macro="list_string_san"/> 75 <expand macro="list_string_san" name="boundary_selection_method"/>
78 </param> 76 </param>
79 <section name="PeakPickerMRM" title="" help="" expanded="false"> 77 <section name="PeakPickerMRM" title="" help="" expanded="false">
80 <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/> 78 <param name="sgolay_frame_length" argument="-algorithm:PeakPickerMRM:sgolay_frame_length" type="integer" optional="true" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
81 <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/> 79 <param name="sgolay_polynomial_order" argument="-algorithm:PeakPickerMRM:sgolay_polynomial_order" type="integer" optional="true" value="3" label="Order of the polynomial that is fitted" help=""/>
82 <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/> 80 <param name="gauss_width" argument="-algorithm:PeakPickerMRM:gauss_width" type="float" optional="true" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
85 <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> 83 <param name="signal_to_noise" argument="-algorithm:PeakPickerMRM:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
86 <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/> 84 <param name="sn_win_len" argument="-algorithm:PeakPickerMRM:sn_win_len" type="float" optional="true" value="1000.0" label="Signal to noise window length" help=""/>
87 <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/> 85 <param name="sn_bin_count" argument="-algorithm:PeakPickerMRM:sn_bin_count" type="integer" optional="true" value="30" label="Signal to noise bin count" help=""/>
88 <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/> 86 <param name="write_sn_log_messages" argument="-algorithm:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
89 <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/> 87 <param name="remove_overlapping_peaks" argument="-algorithm:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
90 <param name="method" argument="-algorithm:PeakPickerMRM:method" display="radio" type="select" optional="false" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help=""> 88 <param name="method" argument="-algorithm:PeakPickerMRM:method" type="select" optional="true" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
91 <option value="legacy">legacy</option> 89 <option value="legacy">legacy</option>
92 <option value="corrected" selected="true">corrected</option> 90 <option value="corrected" selected="true">corrected</option>
93 <option value="crawdad">crawdad</option> 91 <option value="crawdad">crawdad</option>
94 <expand macro="list_string_san"/> 92 <expand macro="list_string_san" name="method"/>
95 </param> 93 </param>
96 </section> 94 </section>
97 <section name="PeakIntegrator" title="" help="" expanded="false"> 95 <section name="PeakIntegrator" title="" help="" expanded="false">
98 <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" display="radio" type="select" optional="false" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help=""> 96 <param name="integration_type" argument="-algorithm:PeakIntegrator:integration_type" type="select" optional="true" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
99 <option value="intensity_sum" selected="true">intensity_sum</option> 97 <option value="intensity_sum" selected="true">intensity_sum</option>
100 <option value="simpson">simpson</option> 98 <option value="simpson">simpson</option>
101 <option value="trapezoid">trapezoid</option> 99 <option value="trapezoid">trapezoid</option>
102 <expand macro="list_string_san"/> 100 <expand macro="list_string_san" name="integration_type"/>
103 </param> 101 </param>
104 <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" display="radio" type="select" optional="false" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)"> 102 <param name="baseline_type" argument="-algorithm:PeakIntegrator:baseline_type" type="select" optional="true" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
105 <option value="base_to_base" selected="true">base_to_base</option> 103 <option value="base_to_base" selected="true">base_to_base</option>
106 <option value="vertical_division">vertical_division</option> 104 <option value="vertical_division">vertical_division</option>
107 <option value="vertical_division_min">vertical_division_min</option> 105 <option value="vertical_division_min">vertical_division_min</option>
108 <option value="vertical_division_max">vertical_division_max</option> 106 <option value="vertical_division_max">vertical_division_max</option>
109 <expand macro="list_string_san"/> 107 <expand macro="list_string_san" name="baseline_type"/>
110 </param> 108 </param>
111 <param name="fit_EMG" argument="-algorithm:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/> 109 <param name="fit_EMG" argument="-algorithm:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
112 </section> 110 </section>
113 </section> 111 </section>
114 <expand macro="adv_opts_macro"> 112 <expand macro="adv_opts_macro">
115 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 113 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
116 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 114 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
117 <expand macro="list_string_san"/> 115 <expand macro="list_string_san" name="test"/>
118 </param> 116 </param>
119 </expand> 117 </expand>
120 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 118 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
121 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 119 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
122 </param> 120 </param>
125 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 123 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
126 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 124 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
127 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 125 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
128 </data> 126 </data>
129 </outputs> 127 </outputs>
130 <tests> 128 <tests><!-- UTILS_MRMTransitionGroupPicker_test_1 -->
131 <expand macro="autotest_MRMTransitionGroupPicker"/> 129 <test expect_num_outputs="2">
132 <expand macro="manutest_MRMTransitionGroupPicker"/> 130 <section name="adv_opts">
131 <param name="force" value="false"/>
132 <param name="test" value="true"/>
133 </section>
134 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
135 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
136 <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
137 <section name="algorithm">
138 <param name="stop_after_feature" value="-1"/>
139 <param name="stop_after_intensity_ratio" value="0.0001"/>
140 <param name="min_peak_width" value="0.001"/>
141 <param name="peak_integration" value="original"/>
142 <param name="background_subtraction" value="none"/>
143 <param name="recalculate_peaks" value="false"/>
144 <param name="use_precursors" value="false"/>
145 <param name="use_consensus" value="true"/>
146 <param name="recalculate_peaks_max_z" value="1.0"/>
147 <param name="minimal_quality" value="-10000.0"/>
148 <param name="resample_boundary" value="15.0"/>
149 <param name="compute_peak_quality" value="false"/>
150 <param name="compute_peak_shape_metrics" value="false"/>
151 <param name="compute_total_mi" value="false"/>
152 <param name="boundary_selection_method" value="largest"/>
153 <section name="PeakPickerMRM">
154 <param name="sgolay_frame_length" value="15"/>
155 <param name="sgolay_polynomial_order" value="3"/>
156 <param name="gauss_width" value="50.0"/>
157 <param name="use_gauss" value="true"/>
158 <param name="peak_width" value="40.0"/>
159 <param name="signal_to_noise" value="1.0"/>
160 <param name="sn_win_len" value="1000.0"/>
161 <param name="sn_bin_count" value="30"/>
162 <param name="write_sn_log_messages" value="false"/>
163 <param name="remove_overlapping_peaks" value="true"/>
164 <param name="method" value="legacy"/>
165 </section>
166 <section name="PeakIntegrator">
167 <param name="integration_type" value="intensity_sum"/>
168 <param name="baseline_type" value="base_to_base"/>
169 <param name="fit_EMG" value="false"/>
170 </section>
171 </section>
172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
173 <output name="ctd_out" ftype="xml">
174 <assert_contents>
175 <is_valid_xml/>
176 </assert_contents>
177 </output>
178 </test>
179 <!-- UTILS_MRMTransitionGroupPicker_test_2 -->
180 <test expect_num_outputs="2">
181 <section name="adv_opts">
182 <param name="force" value="false"/>
183 <param name="test" value="true"/>
184 </section>
185 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
186 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
187 <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
188 <section name="algorithm">
189 <param name="stop_after_feature" value="-1"/>
190 <param name="stop_after_intensity_ratio" value="0.0001"/>
191 <param name="min_peak_width" value="0.001"/>
192 <param name="peak_integration" value="original"/>
193 <param name="background_subtraction" value="none"/>
194 <param name="recalculate_peaks" value="false"/>
195 <param name="use_precursors" value="false"/>
196 <param name="use_consensus" value="true"/>
197 <param name="recalculate_peaks_max_z" value="1.0"/>
198 <param name="minimal_quality" value="-10000.0"/>
199 <param name="resample_boundary" value="15.0"/>
200 <param name="compute_peak_quality" value="false"/>
201 <param name="compute_peak_shape_metrics" value="false"/>
202 <param name="compute_total_mi" value="true"/>
203 <param name="boundary_selection_method" value="largest"/>
204 <section name="PeakPickerMRM">
205 <param name="sgolay_frame_length" value="15"/>
206 <param name="sgolay_polynomial_order" value="3"/>
207 <param name="gauss_width" value="50.0"/>
208 <param name="use_gauss" value="true"/>
209 <param name="peak_width" value="40.0"/>
210 <param name="signal_to_noise" value="1.0"/>
211 <param name="sn_win_len" value="1000.0"/>
212 <param name="sn_bin_count" value="30"/>
213 <param name="write_sn_log_messages" value="false"/>
214 <param name="remove_overlapping_peaks" value="true"/>
215 <param name="method" value="legacy"/>
216 </section>
217 <section name="PeakIntegrator">
218 <param name="integration_type" value="intensity_sum"/>
219 <param name="baseline_type" value="base_to_base"/>
220 <param name="fit_EMG" value="false"/>
221 </section>
222 </section>
223 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
224 <output name="ctd_out" ftype="xml">
225 <assert_contents>
226 <is_valid_xml/>
227 </assert_contents>
228 </output>
229 </test>
133 </tests> 230 </tests>
134 <help><![CDATA[Picks peaks in SRM/MRM chromatograms. 231 <help><![CDATA[Picks peaks in SRM/MRM chromatograms.
135 232
136 233
137 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MRMTransitionGroupPicker.html]]></help> 234 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MRMTransitionGroupPicker.html]]></help>
138 <expand macro="references"/> 235 <expand macro="references"/>
139 </tool> 236 </tool>