Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

comparison MRMTransitionGroupPicker.xml @ 9:cf352aac62b4 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 12:42:24 +0000
parents d88d659e7d2c
children a9000c129043
comparison
equal deleted inserted replaced
8:24e3a7f0277c 9:cf352aac62b4
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="2.3.0"> 4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
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[MRMTransitionGroupPicker 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_tr: 21 mkdir tr &&
19 -tr $param_tr 22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
20 #end if 23 mkdir out &&
21 #if $param_out: 24
22 -out $param_out 25 ## Main program call
23 #end if 26
24 #if $param_algorithm_stop_after_feature: 27 set -o pipefail &&
25 -algorithm:stop_after_feature $param_algorithm_stop_after_feature 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_algorithm_stop_after_intensity_ratio: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio 31 -in
29 #end if 32 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
30 #if $param_algorithm_PeakPickerMRM_sgolay_frame_length: 33 -tr
31 -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length 34 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
32 #end if 35 -out
33 #if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order: 36 'out/output.${gxy2omsext("featurexml")}'
34 -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order 37
35 #end if 38 ## Postprocessing
36 #if $param_algorithm_PeakPickerMRM_gauss_width: 39 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
37 -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 #end if 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 #if $param_algorithm_PeakPickerMRM_use_gauss: 42 #end if]]></command>
40 -algorithm:PeakPickerMRM:use_gauss 43 <configfiles>
41 #if " " in str($param_algorithm_PeakPickerMRM_use_gauss): 44 <inputs name="args_json" data_style="paths"/>
42 "$param_algorithm_PeakPickerMRM_use_gauss" 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 #else 46 </configfiles>
44 $param_algorithm_PeakPickerMRM_use_gauss
45 #end if
46 #end if
47 #if $param_algorithm_PeakPickerMRM_peak_width:
48 -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
49 #end if
50 #if $param_algorithm_PeakPickerMRM_signal_to_noise:
51 -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise
52 #end if
53 #if $param_algorithm_PeakPickerMRM_sn_win_len:
54 -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len
55 #end if
56 #if $param_algorithm_PeakPickerMRM_sn_bin_count:
57 -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
58 #end if
59 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
60 -algorithm:PeakPickerMRM:write_sn_log_messages
61 #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages):
62 "$param_algorithm_PeakPickerMRM_write_sn_log_messages"
63 #else
64 $param_algorithm_PeakPickerMRM_write_sn_log_messages
65 #end if
66 #end if
67 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
68 -algorithm:PeakPickerMRM:remove_overlapping_peaks
69 #end if
70 #if $param_algorithm_PeakPickerMRM_method:
71 -algorithm:PeakPickerMRM:method
72 #if " " in str($param_algorithm_PeakPickerMRM_method):
73 "$param_algorithm_PeakPickerMRM_method"
74 #else
75 $param_algorithm_PeakPickerMRM_method
76 #end if
77 #end if
78 #if $adv_opts.adv_opts_selector=='advanced':
79 #if $adv_opts.param_force:
80 -force
81 #end if
82 #if $adv_opts.param_algorithm_min_peak_width:
83 -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
84 #end if
85 #if $adv_opts.param_algorithm_background_subtraction:
86 -algorithm:background_subtraction
87 #if " " in str($adv_opts.param_algorithm_background_subtraction):
88 "$adv_opts.param_algorithm_background_subtraction"
89 #else
90 $adv_opts.param_algorithm_background_subtraction
91 #end if
92 #end if
93 #if $adv_opts.param_algorithm_recalculate_peaks:
94 -algorithm:recalculate_peaks
95 #end if
96 #if $adv_opts.param_algorithm_use_precursors:
97 -algorithm:use_precursors
98 #end if
99 #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
100 -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
101 #end if
102 #if $adv_opts.param_algorithm_minimal_quality:
103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
104 #end if
105 #if $adv_opts.param_algorithm_resample_boundary:
106 -algorithm:resample_boundary $adv_opts.param_algorithm_resample_boundary
107 #end if
108 #if $adv_opts.param_algorithm_compute_peak_quality:
109 -algorithm:compute_peak_quality
110 #end if
111 #end if
112 ]]></command>
113 <inputs> 47 <inputs>
114 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/> 48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
115 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/> 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)"/>
116 <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/> 50 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
117 <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/> 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=""/>
118 <param name="param_algorithm_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/> 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=""/>
119 <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> 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=""/>
120 <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> 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="">
121 <param name="param_algorithm_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "> 55 <option value="original" selected="true">original</option>
122 <option value="false">false</option> 56 <option value="smoothed">smoothed</option>
123 <option value="true" selected="true">true</option> 57 <expand macro="list_string_san"/>
58 </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">
60 <option value="none" selected="true">none</option>
61 <option value="original">original</option>
62 <option value="exact">exact</option>
63 <expand macro="list_string_san"/>
64 </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"/>
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=""/>
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=""/>
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)"/>
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=""/>
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=""/>
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"/>
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"/>
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=""/>
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="">
75 <option value="largest" selected="true">largest</option>
76 <option value="widest">widest</option>
77 <expand macro="list_string_san"/>
78 </param>
79 <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"/>
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=""/>
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=""/>
83 <param name="use_gauss" argument="-algorithm:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
84 <param name="peak_width" argument="-algorithm:PeakPickerMRM:peak_width" type="float" optional="true" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
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"/>
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=""/>
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=""/>
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=""/>
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=""/>
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="">
91 <option value="legacy">legacy</option>
92 <option value="corrected" selected="true">corrected</option>
93 <option value="crawdad">crawdad</option>
94 <expand macro="list_string_san"/>
95 </param>
96 </section>
97 <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="">
99 <option value="intensity_sum" selected="true">intensity_sum</option>
100 <option value="simpson">simpson</option>
101 <option value="trapezoid">trapezoid</option>
102 <expand macro="list_string_san"/>
103 </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)">
105 <option value="base_to_base" selected="true">base_to_base</option>
106 <option value="vertical_division">vertical_division</option>
107 <option value="vertical_division_min">vertical_division_min</option>
108 <option value="vertical_division_max">vertical_division_max</option>
109 <expand macro="list_string_san"/>
110 </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=""/>
112 </section>
113 </section>
114 <expand macro="adv_opts_macro">
115 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
117 <expand macro="list_string_san"/>
118 </param>
119 </expand>
120 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
121 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
124 </param> 122 </param>
125 <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
126 <param name="param_algorithm_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
127 <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
128 <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
129 <param name="param_algorithm_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) ">
130 <option value="true" selected="true">true</option>
131 <option value="false">false</option>
132 </param>
133 <param name="param_algorithm_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
134 <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" 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="(-method) ">
135 <option value="legacy">legacy</option>
136 <option value="corrected" selected="true">corrected</option>
137 <option value="crawdad">crawdad</option>
138 </param>
139 <expand macro="advanced_options">
140 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
141 <param name="param_algorithm_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
142 <param name="param_algorithm_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
143 <option value="none" selected="true">none</option>
144 <option value="smoothed">smoothed</option>
145 <option value="original">original</option>
146 </param>
147 <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
148 <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
149 <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
150 <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
151 <param name="param_algorithm_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
152 <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
153 </expand>
154 </inputs> 123 </inputs>
155 <outputs> 124 <outputs>
156 <data name="param_out" format="featurexml"/> 125 <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">
127 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
128 </data>
157 </outputs> 129 </outputs>
158 <help>Picks peaks in SRM/MRM chromatograms. 130 <tests>
131 <expand macro="autotest_MRMTransitionGroupPicker"/>
132 <expand macro="manutest_MRMTransitionGroupPicker"/>
133 </tests>
134 <help><![CDATA[Picks peaks in SRM/MRM chromatograms.
159 135
160 136
161 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MRMTransitionGroupPicker.html</help> 137 For more information, visit http://www.openms.de/documentation/UTILS_MRMTransitionGroupPicker.html]]></help>
138 <expand macro="references"/>
162 </tool> 139 </tool>