Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker

comparison MRMTransitionGroupPicker.xml @ 1:289009115eb2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:27:49 -0400
parents 2c8729a286ea
children 7dca11634139
comparison
equal deleted inserted replaced
0:2c8729a286ea 1:289009115eb2
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"/>
34 #end if 35 #end if
35 #if $param_algorithm_PeakPickerMRM_gauss_width: 36 #if $param_algorithm_PeakPickerMRM_gauss_width:
36 -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width 37 -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
37 #end if 38 #end if
38 #if $param_algorithm_PeakPickerMRM_use_gauss: 39 #if $param_algorithm_PeakPickerMRM_use_gauss:
39 -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss 40 -algorithm:PeakPickerMRM:use_gauss
41 #if " " in str($param_algorithm_PeakPickerMRM_use_gauss):
42 "$param_algorithm_PeakPickerMRM_use_gauss"
43 #else
44 $param_algorithm_PeakPickerMRM_use_gauss
45 #end if
40 #end if 46 #end if
41 #if $param_algorithm_PeakPickerMRM_peak_width: 47 #if $param_algorithm_PeakPickerMRM_peak_width:
42 -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width 48 -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
43 #end if 49 #end if
44 #if $param_algorithm_PeakPickerMRM_signal_to_noise: 50 #if $param_algorithm_PeakPickerMRM_signal_to_noise:
49 #end if 55 #end if
50 #if $param_algorithm_PeakPickerMRM_sn_bin_count: 56 #if $param_algorithm_PeakPickerMRM_sn_bin_count:
51 -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count 57 -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
52 #end if 58 #end if
53 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages: 59 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
54 -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages 60 -algorithm:PeakPickerMRM:write_sn_log_messages
61 #if " " in str($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
55 #end if 66 #end if
56 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks: 67 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
57 -algorithm:PeakPickerMRM:remove_overlapping_peaks 68 -algorithm:PeakPickerMRM:remove_overlapping_peaks
58 #end if 69 #end if
59 #if $param_algorithm_PeakPickerMRM_method: 70 #if $param_algorithm_PeakPickerMRM_method:
60 -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method 71 -algorithm:PeakPickerMRM:method
72 #if " " in str($param_algorithm_PeakPickerMRM_method):
73 "$param_algorithm_PeakPickerMRM_method"
74 #else
75 $param_algorithm_PeakPickerMRM_method
76 #end if
61 #end if 77 #end if
62 #if $adv_opts.adv_opts_selector=='advanced': 78 #if $adv_opts.adv_opts_selector=='advanced':
63 #if $adv_opts.param_force: 79 #if $adv_opts.param_force:
64 -force 80 -force
65 #end if 81 #end if
66 #if $adv_opts.param_algorithm_min_peak_width: 82 #if $adv_opts.param_algorithm_min_peak_width:
67 -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width 83 -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
68 #end if 84 #end if
69 #if $adv_opts.param_algorithm_background_subtraction: 85 #if $adv_opts.param_algorithm_background_subtraction:
70 -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction 86 -algorithm:background_subtraction
87 #if " " in str($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
71 #end if 92 #end if
72 #if $adv_opts.param_algorithm_recalculate_peaks: 93 #if $adv_opts.param_algorithm_recalculate_peaks:
73 -algorithm:recalculate_peaks "$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
74 #end if 98 #end if
75 #if $adv_opts.param_algorithm_recalculate_peaks_max_z: 99 #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
76 -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
77 #end if 101 #end if
78 #if $adv_opts.param_algorithm_minimal_quality: 102 #if $adv_opts.param_algorithm_minimal_quality:
79 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality 103 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
80 #end if 104 #end if
81 #if $adv_opts.param_algorithm_compute_peak_quality: 105 #if $adv_opts.param_algorithm_compute_peak_quality:
82 -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality" 106 -algorithm:compute_peak_quality
83 #end if 107 #end if
84 #end if 108 #end if
85 </command> 109 </command>
86 <inputs> 110 <inputs>
87 <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) "/>
115 <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">
116 <option value="none" selected="true">none</option> 140 <option value="none" selected="true">none</option>
117 <option value="smoothed">smoothed</option> 141 <option value="smoothed">smoothed</option>
118 <option value="original">original</option> 142 <option value="original">original</option>
119 </param> 143 </param>
120 <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"/>
121 <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) "/>
122 <valid initial="string.printable">
123 <remove value="'"/>
124 <remove value="&quot;"/>
125 </valid>
126 </sanitizer>
127 </param>
128 <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)"/>
129 <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) "/>
130 <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"/>
131 <sanitizer>
132 <valid initial="string.printable">
133 <remove value="'"/>
134 <remove value="&quot;"/>
135 </valid>
136 </sanitizer>
137 </param>
138 </expand> 149 </expand>
139 </inputs> 150 </inputs>
140 <outputs> 151 <outputs>
141 <data name="param_out" format="featurexml"/> 152 <data name="param_out" format="featurexml"/>
142 </outputs> 153 </outputs>
143 <help>None 154 <help>Picks peaks in SRM/MRM chromatograms.
144 155
145 156
146 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>
147 </tool> 158 </tool>