Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

comparison MRMTransitionGroupPicker.xml @ 3:4b87a29bf4e2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 18:55:21 -0400
parents 96c52704abcd
children b391dc9a5863
comparison
equal deleted inserted replaced
2:42ff199c97a8 3:4b87a29bf4e2
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 CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.1.0"> 4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.2.0">
5 <description>Picks peaks in SRM/MRM chromatograms.</description>
5 <macros> 6 <macros>
6 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token> 7 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
7 <import>macros.xml</import> 8 <import>macros.xml</import>
8 </macros> 9 </macros>
9 <expand macro="references"/> 10 <expand macro="references"/>
88 #else 89 #else
89 $adv_opts.param_algorithm_background_subtraction 90 $adv_opts.param_algorithm_background_subtraction
90 #end if 91 #end if
91 #end if 92 #end if
92 #if $adv_opts.param_algorithm_recalculate_peaks: 93 #if $adv_opts.param_algorithm_recalculate_peaks:
93 -algorithm:recalculate_peaks "$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
94 #end if 98 #end if
95 #if $adv_opts.param_algorithm_recalculate_peaks_max_z: 99 #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
96 -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z 100 -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
97 #end if 101 #end if
98 #if $adv_opts.param_algorithm_minimal_quality: 102 #if $adv_opts.param_algorithm_minimal_quality:
99 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality 103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
100 #end if 104 #end if
101 #if $adv_opts.param_algorithm_compute_peak_quality: 105 #if $adv_opts.param_algorithm_compute_peak_quality:
102 -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality" 106 -algorithm:compute_peak_quality
103 #end if 107 #end if
104 #end if 108 #end if
105 </command> 109 </command>
106 <inputs> 110 <inputs>
107 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/> 111 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
135 <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"> 139 <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">
136 <option value="none" selected="true">none</option> 140 <option value="none" selected="true">none</option>
137 <option value="smoothed">smoothed</option> 141 <option value="smoothed">smoothed</option>
138 <option value="original">original</option> 142 <option value="original">original</option>
139 </param> 143 </param>
140 <param name="param_algorithm_recalculate_peaks" type="text" size="30" value="false" 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"> 144 <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"/>
141 <sanitizer> 145 <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) "/>
142 <valid initial="string.printable">
143 <remove value="'"/>
144 <remove value="&quot;"/>
145 </valid>
146 </sanitizer>
147 </param>
148 <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)"/> 146 <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)"/>
149 <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) "/> 147 <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) "/>
150 <param name="param_algorithm_compute_peak_quality" type="text" size="30" value="false" 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"> 148 <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"/>
151 <sanitizer>
152 <valid initial="string.printable">
153 <remove value="'"/>
154 <remove value="&quot;"/>
155 </valid>
156 </sanitizer>
157 </param>
158 </expand> 149 </expand>
159 </inputs> 150 </inputs>
160 <outputs> 151 <outputs>
161 <data name="param_out" format="featurexml"/> 152 <data name="param_out" format="featurexml"/>
162 </outputs> 153 </outputs>
163 <help>None 154 <help>Picks peaks in SRM/MRM chromatograms.
164 155
165 156
166 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html</help> 157 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html</help>
167 </tool> 158 </tool>