comparison MRMTransitionGroupPicker.xml @ 0:2c8729a286ea draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:38:23 -0500
parents
children 289009115eb2
comparison
equal deleted inserted replaced
-1:000000000000 0:2c8729a286ea
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.1.0">
5 <macros>
6 <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
7 <import>macros.xml</import>
8 </macros>
9 <expand macro="references"/>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>MRMTransitionGroupPicker
13
14 #if $param_in:
15 -in $param_in
16 #end if
17 #if $param_tr:
18 -tr $param_tr
19 #end if
20 #if $param_out:
21 -out $param_out
22 #end if
23 #if $param_algorithm_stop_after_feature:
24 -algorithm:stop_after_feature $param_algorithm_stop_after_feature
25 #end if
26 #if $param_algorithm_stop_after_intensity_ratio:
27 -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio
28 #end if
29 #if $param_algorithm_PeakPickerMRM_sgolay_frame_length:
30 -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length
31 #end if
32 #if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order:
33 -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order
34 #end if
35 #if $param_algorithm_PeakPickerMRM_gauss_width:
36 -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
37 #end if
38 #if $param_algorithm_PeakPickerMRM_use_gauss:
39 -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss
40 #end if
41 #if $param_algorithm_PeakPickerMRM_peak_width:
42 -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
43 #end if
44 #if $param_algorithm_PeakPickerMRM_signal_to_noise:
45 -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise
46 #end if
47 #if $param_algorithm_PeakPickerMRM_sn_win_len:
48 -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len
49 #end if
50 #if $param_algorithm_PeakPickerMRM_sn_bin_count:
51 -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
52 #end if
53 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
54 -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages
55 #end if
56 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
57 -algorithm:PeakPickerMRM:remove_overlapping_peaks
58 #end if
59 #if $param_algorithm_PeakPickerMRM_method:
60 -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method
61 #end if
62 #if $adv_opts.adv_opts_selector=='advanced':
63 #if $adv_opts.param_force:
64 -force
65 #end if
66 #if $adv_opts.param_algorithm_min_peak_width:
67 -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
68 #end if
69 #if $adv_opts.param_algorithm_background_subtraction:
70 -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction
71 #end if
72 #if $adv_opts.param_algorithm_recalculate_peaks:
73 -algorithm:recalculate_peaks "$adv_opts.param_algorithm_recalculate_peaks"
74 #end if
75 #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
76 -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
77 #end if
78 #if $adv_opts.param_algorithm_minimal_quality:
79 -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
80 #end if
81 #if $adv_opts.param_algorithm_compute_peak_quality:
82 -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality"
83 #end if
84 #end if
85 </command>
86 <inputs>
87 <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
88 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
89 <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) "/>
90 <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
91 <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"/>
92 <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
93 <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
94 <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) ">
95 <option value="false">false</option>
96 <option value="true" selected="true">true</option>
97 </param>
98 <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"/>
99 <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"/>
100 <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
101 <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
102 <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) ">
103 <option value="true" selected="true">true</option>
104 <option value="false">false</option>
105 </param>
106 <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) "/>
107 <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) ">
108 <option value="legacy" selected="true">legacy</option>
109 <option value="corrected">corrected</option>
110 <option value="crawdad">crawdad</option>
111 </param>
112 <expand macro="advanced_options">
113 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
114 <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) "/>
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">
116 <option value="none" selected="true">none</option>
117 <option value="smoothed">smoothed</option>
118 <option value="original">original</option>
119 </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">
121 <sanitizer>
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)"/>
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) "/>
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">
131 <sanitizer>
132 <valid initial="string.printable">
133 <remove value="'"/>
134 <remove value="&quot;"/>
135 </valid>
136 </sanitizer>
137 </param>
138 </expand>
139 </inputs>
140 <outputs>
141 <data name="param_out" format="featurexml"/>
142 </outputs>
143 <help>None
144
145
146 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html</help>
147 </tool>