Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

comparison MRMTransitionGroupPicker.xml @ 5:7dca11634139 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:01:09 -0500
parents 289009115eb2
children d88d659e7d2c
comparison
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4:d21ae981ab53 5:7dca11634139
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.2.0"> 4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.3.0">
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 </macros> 9 </macros>
100 -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
101 #end if 101 #end if
102 #if $adv_opts.param_algorithm_minimal_quality: 102 #if $adv_opts.param_algorithm_minimal_quality:
103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality 103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
104 #end if 104 #end if
105 #if $adv_opts.param_algorithm_resample_boundary:
106 -algorithm:resample_boundary $adv_opts.param_algorithm_resample_boundary
107 #end if
105 #if $adv_opts.param_algorithm_compute_peak_quality: 108 #if $adv_opts.param_algorithm_compute_peak_quality:
106 -algorithm:compute_peak_quality 109 -algorithm:compute_peak_quality
107 #end if 110 #end if
108 #end if 111 #end if
109 </command> 112 </command>
117 <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> 120 <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
118 <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) "> 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) ">
119 <option value="false">false</option> 122 <option value="false">false</option>
120 <option value="true" selected="true">true</option> 123 <option value="true" selected="true">true</option>
121 </param> 124 </param>
122 <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="40.0" 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"/> 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"/>
123 <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"/> 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"/>
124 <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/> 127 <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
125 <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/> 128 <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
126 <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) "> 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) ">
127 <option value="true" selected="true">true</option> 130 <option value="true" selected="true">true</option>
128 <option value="false">false</option> 131 <option value="false">false</option>
129 </param> 132 </param>
130 <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) "/> 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) "/>
131 <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) "> 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) ">
132 <option value="legacy" selected="true">legacy</option> 135 <option value="legacy">legacy</option>
133 <option value="corrected">corrected</option> 136 <option value="corrected" selected="true">corrected</option>
134 <option value="crawdad">crawdad</option> 137 <option value="crawdad">crawdad</option>
135 </param> 138 </param>
136 <expand macro="advanced_options"> 139 <expand macro="advanced_options">
137 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 140 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
138 <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) "/> 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) "/>
143 </param> 146 </param>
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"/> 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"/>
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) "/> 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) "/>
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_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)"/>
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_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) "/>
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"/> 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"/>
149 </expand> 153 </expand>
150 </inputs> 154 </inputs>
151 <outputs> 155 <outputs>
152 <data name="param_out" format="featurexml"/> 156 <data name="param_out" format="featurexml"/>