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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="1.12.0"> 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 <description>Picks peaks and finds features in an SRM experiment.</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.0.0">
5 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> 5 <description>Picks peaks and finds features in an SRM experiment.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>OpenSwathAnalyzer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>OpenSwathAnalyzer
11 14
12 -in ${param_in} 15 #if $param_in:
13 -tr ${param_tr} 16 -in $param_in
14 -rt_norm ${param_rt_norm} 17 #end if
15 -out ${param_out} 18 #if $param_tr:
16 ${param_no-strict} 19 -tr $param_tr
17 -swath_files ${param_swath_files} 20 #end if
18 -min_upper_edge_dist ${param_min_upper_edge_dist} 21 #if $param_rt_norm:
19 -threads \${GALAXY_SLOTS:-24} 22 -rt_norm $param_rt_norm
20 -algorithm:stop_report_after_feature ${param_stop_report_after_feature} 23 #end if
21 -algorithm:rt_extraction_window ${param_rt_extraction_window} 24 #if $param_out:
22 -algorithm:rt_normalization_factor ${param_rt_normalization_factor} 25 -out $param_out
23 -algorithm:TransitionGroupPicker:stop_after_feature ${param_stop_after_feature} 26 #end if
24 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio ${param_stop_after_intensity_ratio} 27 #if $param_no_strict:
25 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length ${param_sgolay_frame_length} 28 -no-strict
26 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order ${param_sgolay_polynomial_order} 29 #end if
27 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width ${param_gauss_width} 30 -swath_files
28 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss ${param_use_gauss} 31 #for token in $param_swath_files:
29 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width ${param_peak_width} 32 $token
30 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise ${param_signal_to_noise} 33 #end for
31 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len ${param_sn_win_len} 34 #if $param_min_upper_edge_dist:
32 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count ${param_sn_bin_count} 35 -min_upper_edge_dist $param_min_upper_edge_dist
33 ${param_remove_overlapping_peaks} 36 #end if
34 -algorithm:TransitionGroupPicker:PeakPickerMRM:method ${param_method} 37 -threads \${GALAXY_SLOTS:-24}
35 -algorithm:DIAScoring:dia_extraction_window ${param_dia_extraction_window} 38 #if $param_algorithm_stop_report_after_feature:
36 ${param_dia_centroided} 39 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
37 -algorithm:DIAScoring:dia_byseries_intensity_min ${param_dia_byseries_intensity_min} 40 #end if
38 -algorithm:DIAScoring:dia_byseries_ppm_diff ${param_dia_byseries_ppm_diff} 41 #if $param_algorithm_rt_extraction_window:
39 -algorithm:DIAScoring:dia_nr_isotopes ${param_dia_nr_isotopes} 42 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
40 -algorithm:DIAScoring:dia_nr_charges ${param_dia_nr_charges} 43 #end if
41 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff ${param_peak_before_mono_max_ppm_diff} 44 #if $param_algorithm_rt_normalization_factor:
45 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
46 #end if
47 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
48 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
49 #end if
50 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
51 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
52 #end if
53 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
54 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
55 #end if
56 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
57 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
58 #end if
59 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
60 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
61 #end if
62 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
63 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
64 #end if
65 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
66 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
67 #end if
68 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
69 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
70 #end if
71 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
72 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
73 #end if
74 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
75 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
76 #end if
77 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
78 -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
79 #end if
80 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
81 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
82 #end if
83 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
84 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
85 #if &quot; &quot; in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
86 &quot;$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method&quot;
87 #else
88 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
89 #end if
90 #end if
91 #if $param_algorithm_DIAScoring_dia_extraction_window:
92 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
93 #end if
94 #if $param_algorithm_DIAScoring_dia_centroided:
95 -algorithm:DIAScoring:dia_centroided
96 #end if
97 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
98 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
99 #end if
100 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
101 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
102 #end if
103 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
104 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
105 #end if
106 #if $param_algorithm_DIAScoring_dia_nr_charges:
107 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
108 #end if
109 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
110 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
111 #end if
42 #if $adv_opts.adv_opts_selector=='advanced': 112 #if $adv_opts.adv_opts_selector=='advanced':
43 -model:type ${adv_opts.param_type} 113 #if $adv_opts.param_force:
44 ${adv_opts.param_symmetric_regression} 114 -force
45 -algorithm:quantification_cutoff ${adv_opts.param_quantification_cutoff} 115 #end if
46 ${adv_opts.param_write_convex_hull} 116 #if $adv_opts.param_model_type:
47 -algorithm:add_up_spectra ${adv_opts.param_add_up_spectra} 117 -model:type
48 -algorithm:spacing_for_spectra_resampling ${adv_opts.param_spacing_for_spectra_resampling} 118 #if &quot; &quot; in str($adv_opts.param_model_type):
49 -algorithm:TransitionGroupPicker:min_peak_width ${adv_opts.param_min_peak_width} 119 &quot;$adv_opts.param_model_type&quot;
50 -algorithm:TransitionGroupPicker:background_subtraction ${adv_opts.param_background_subtraction} 120 #else
51 -algorithm:TransitionGroupPicker:recalculate_peaks ${adv_opts.param_recalculate_peaks} 121 $adv_opts.param_model_type
52 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z ${adv_opts.param_recalculate_peaks_max_z} 122 #end if
53 -algorithm:TransitionGroupPicker:minimal_quality ${adv_opts.param_minimal_quality} 123 #end if
54 -algorithm:TransitionGroupPicker:compute_peak_quality ${adv_opts.param_compute_peak_quality} 124 #if $adv_opts.param_model_symmetric_regression:
55 -algorithm:EMGScoring:interpolation_step ${adv_opts.param_interpolation_step} 125 -model:symmetric_regression
56 -algorithm:EMGScoring:tolerance_stdev_bounding_box ${adv_opts.param_tolerance_stdev_bounding_box} 126 #end if
57 -algorithm:EMGScoring:max_iteration ${adv_opts.param_max_iteration} 127 #if $adv_opts.param_algorithm_quantification_cutoff:
58 -algorithm:EMGScoring:statistics:mean ${adv_opts.param_mean} 128 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
59 -algorithm:EMGScoring:statistics:variance ${adv_opts.param_variance} 129 #end if
60 ${adv_opts.param_use_shape_score} 130 #if $adv_opts.param_algorithm_write_convex_hull:
61 ${adv_opts.param_use_coelution_score} 131 -algorithm:write_convex_hull
62 ${adv_opts.param_use_rt_score} 132 #end if
63 ${adv_opts.param_use_library_score} 133 #if $adv_opts.param_algorithm_add_up_spectra:
64 ${adv_opts.param_use_elution_model_score} 134 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
65 ${adv_opts.param_use_intensity_score} 135 #end if
66 ${adv_opts.param_use_nr_peaks_score} 136 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
67 ${adv_opts.param_use_total_xic_score} 137 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
68 ${adv_opts.param_use_sn_score} 138 #end if
69 ${adv_opts.param_use_dia_scores} 139 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
70 ${adv_opts.param_use_ms1_correlation} 140 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
71 ${adv_opts.param_use_ms1_fullscan} 141 #end if
142 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
143 -algorithm:TransitionGroupPicker:background_subtraction
144 #if &quot; &quot; in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
145 &quot;$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction&quot;
146 #else
147 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
148 #end if
149 #end if
150 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
151 -algorithm:TransitionGroupPicker:recalculate_peaks &quot;$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks&quot;
152 #end if
153 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
154 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
155 #end if
156 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
157 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
158 #end if
159 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
160 -algorithm:TransitionGroupPicker:compute_peak_quality &quot;$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality&quot;
161 #end if
162 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
163 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
164 #end if
165 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
166 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
167 #end if
168 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
169 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
170 #end if
171 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
172 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
173 #end if
174 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
175 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
176 #end if
177 #if $adv_opts.param_algorithm_Scores_use_shape_score:
178 -algorithm:Scores:use_shape_score
179 #end if
180 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
181 -algorithm:Scores:use_coelution_score
182 #end if
183 #if $adv_opts.param_algorithm_Scores_use_rt_score:
184 -algorithm:Scores:use_rt_score
185 #end if
186 #if $adv_opts.param_algorithm_Scores_use_library_score:
187 -algorithm:Scores:use_library_score
188 #end if
189 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
190 -algorithm:Scores:use_elution_model_score
191 #end if
192 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
193 -algorithm:Scores:use_intensity_score
194 #end if
195 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
196 -algorithm:Scores:use_nr_peaks_score
197 #end if
198 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
199 -algorithm:Scores:use_total_xic_score
200 #end if
201 #if $adv_opts.param_algorithm_Scores_use_sn_score:
202 -algorithm:Scores:use_sn_score
203 #end if
204 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
205 -algorithm:Scores:use_dia_scores
206 #end if
207 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
208 -algorithm:Scores:use_ms1_correlation
209 #end if
210 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
211 -algorithm:Scores:use_ms1_fullscan
212 #end if
72 #end if 213 #end if
73 </command> 214 </command>
74 <inputs> 215 <inputs>
75 <param name="param_in" type="data" format="mzML" optional="False" label="input file containing the chromatograms." help="(-in)"/> 216 <param format="mzml" help="(-in) " label="input file containing the chromatograms" name="param_in" optional="False" type="data"/>
76 <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/> 217 <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/>
77 <param name="param_rt_norm" type="data" format="" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm)"/> 218 <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
78 <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/> 219 <param checked="false" falsevalue="" help="(-no-strict) " label="run in non-strict mode and allow some chromatograms to not be mapped" name="param_no_strict" optional="True" truevalue="-no-strict" type="boolean"/>
79 <param name="param_swath_files" type="data" format="mzML" optional="True" size="20" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions. If present, SWATH specific scoring will be used." help="(-swath_files)"/> 220 <param format="mzml" help="(-swath_files) If present, SWATH specific scoring will be used" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" multiple="true" name="param_swath_files" optional="True" size="30" type="data">
80 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist)"/> 221 <sanitizer>
81 <param name="param_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)." help="(-stop_report_after_feature)"/> 222 <valid initial="string.printable">
82 <param name="param_rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution). For this to work, the TraML input file needs to contain normalized RT values." help="(-rt_extraction_window)"/> 223 <remove value="'"/>
83 <param name="param_rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)" help="(-rt_normalization_factor)"/> 224 <remove value="&quot;"/>
84 <param name="param_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)." help="(-stop_after_feature)"/> 225 </valid>
85 <param name="param_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio)"/> 226 </sanitizer>
86 <param name="param_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." help="(-sgolay_frame_length)"/>
87 <param name="param_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted." help="(-sgolay_polynomial_order)"/>
88 <param name="param_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size." help="(-gauss_width)"/>
89 <param name="param_use_gauss" type="text" size="20" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss)"/>
90 <param name="param_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off." help="(-peak_width)"/>
91 <param name="param_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 (e.g. 1.0) can lead to peaks whose flanks are not fully captured." help="(-signal_to_noise)"/>
92 <param name="param_sn_win_len" type="float" value="1000.0" label="Signal to noise window length." help="(-sn_win_len)"/>
93 <param name="param_sn_bin_count" type="integer" value="30" label="Signal to noise bin count." help="(-sn_bin_count)"/>
94 <param name="param_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks true" falsevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks false" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks)"/>
95 <param name="param_method" type="select" optional="True" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)." help="(-method)">
96 <option value="legacy">legacy</option>
97 <option value="corrected">corrected</option>
98 <option value="crawdad">crawdad</option>
99 </param>
100 <param name="param_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th." help="(-dia_extraction_window)"/>
101 <param name="param_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided true" falsevalue="-algorithm:DIAScoring:dia_centroided false" checked="false" optional="True" label="Use centroded DIA data." help="(-dia_centroided)"/>
102 <param name="param_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to consider." help="(-dia_byseries_intensity_min)"/>
103 <param name="param_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to consider." help="(-dia_byseries_ppm_diff)"/>
104 <param name="param_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to consider." help="(-dia_nr_isotopes)"/>
105 <param name="param_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to consider." help="(-dia_nr_charges)"/>
106 <param name="param_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic." help="(-peak_before_mono_max_ppm_diff)"/>
107 <expand macro="advanced_options">
108 <param name="param_type" type="select" optional="True" value="linear" label="Type of model" help="(-type)">
109 <option value="linear">linear</option>
110 <option value="b_spline">b_spline</option>
111 <option value="interpolated">interpolated</option>
112 </param> 227 </param>
113 <param name="param_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression true" falsevalue="-model:symmetric_regression false" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/> 228 <param help="(-min_upper_edge_dist) " label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" name="param_min_upper_edge_dist" type="float" value="0.0"/>
114 <param name="param_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff)"/> 229 <param help="(-stop_report_after_feature) " label="Stop reporting after feature (ordered by quality; -1 means do not stop)" name="param_algorithm_stop_report_after_feature" type="integer" value="-1"/>
115 <param name="param_write_convex_hull" type="boolean" truevalue="-algorithm:write_convex_hull true" falsevalue="-algorithm:write_convex_hull false" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull)"/> 230 <param help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" name="param_algorithm_rt_extraction_window" type="float" value="-1.0"/>
116 <param name="param_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra)"/> 231 <param help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" name="param_algorithm_rt_normalization_factor" type="float" value="1.0"/>
117 <param name="param_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling)"/> 232 <param help="(-stop_after_feature) " label="Stop finding after feature (ordered by intensity; -1 means do not stop)" name="param_algorithm_TransitionGroupPicker_stop_after_feature" type="integer" value="-1"/>
118 <param name="param_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)"/> 233 <param help="(-stop_after_intensity_ratio) " label="Stop after reaching intensity ratio" name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001"/>
119 <param name="param_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental). The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that." help="(-background_subtraction)"> 234 <param help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added" label="The number of subsequent data points used for smoothing" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15"/>
120 <option value="none">none</option> 235 <param help="(-sgolay_polynomial_order) " label="Order of the polynomial that is fitted" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3"/>
121 <option value="smoothed">smoothed</option> 236 <param help="(-gauss_width) " label="Gaussian width in seconds, estimated peak size" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0"/>
122 <option value="original">original</option> 237 <param checked="true" falsevalue="" help="(-use_gauss) " label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean"/>
238 <param help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off" label="Force a certain minimal peak_width on the data (" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0"/>
239 <param help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" min="0.0" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" optional="True" type="float" value="1.0"/>
240 <param help="(-sn_win_len) " label="Signal to noise window length" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0"/>
241 <param help="(-sn_bin_count) " label="Signal to noise bin count" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30"/>
242 <param checked="true" falsevalue="" help="(-write_sn_log_messages) " label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean"/>
243 <param checked="false" falsevalue="" help="(-remove_overlapping_peaks) " label="Try to remove overlapping peaks during peak picking" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean"/>
244 <param help="(-method) " label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" optional="True" type="select" value="legacy">
245 <option value="legacy">legacy</option>
246 <option value="corrected">corrected</option>
247 <option value="crawdad">crawdad</option>
123 </param> 248 </param>
124 <param name="param_recalculate_peaks" type="text" size="20" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks. Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large." help="(-recalculate_peaks)"/> 249 <param help="(-dia_extraction_window) " label="DIA extraction window in Th" min="0.0" name="param_algorithm_DIAScoring_dia_extraction_window" optional="True" type="float" value="0.05"/>
125 <param name="param_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. If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)." help="(-recalculate_peaks_max_z)"/> 250 <param checked="false" falsevalue="" help="(-dia_centroided) " label="Use centroded DIA data" name="param_algorithm_DIAScoring_dia_centroided" optional="True" truevalue="-algorithm:DIAScoring:dia_centroided" type="boolean"/>
126 <param name="param_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)"/> 251 <param help="(-dia_byseries_intensity_min) " label="DIA b/y series minimum intensity to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_intensity_min" optional="True" type="float" value="300.0"/>
127 <param name="param_compute_peak_quality" type="text" size="20" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions. The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad." help="(-compute_peak_quality)"/> 252 <param help="(-dia_byseries_ppm_diff) " label="DIA b/y series minimal difference in ppm to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_ppm_diff" optional="True" type="float" value="10.0"/>
128 <param name="param_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function." help="(-interpolation_step)"/> 253 <param help="(-dia_nr_isotopes) " label="DIA nr of isotopes to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_isotopes" optional="True" type="integer" value="4"/>
129 <param name="param_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data." help="(-tolerance_stdev_bounding_box)"/> 254 <param help="(-dia_nr_charges) " label="DIA nr of charges to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_charges" optional="True" type="integer" value="4"/>
130 <param name="param_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm." help="(-max_iteration)"/> 255 <param help="(-peak_before_mono_max_ppm_diff) " label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" min="0.0" name="param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff" optional="True" type="float" value="20.0"/>
131 <param name="param_mean" type="float" value="1.0" label="Centroid position of the model." help="(-mean)"/> 256 <expand macro="advanced_options">
132 <param name="param_variance" type="float" value="1.0" label="Variance of the model." help="(-variance)"/> 257 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
133 <param name="param_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score true" falsevalue="-algorithm:Scores:use_shape_score false" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score)"/> 258 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear">
134 <param name="param_use_coelution_score" type="boolean" truevalue="-algorithm:Scores:use_coelution_score true" falsevalue="-algorithm:Scores:use_coelution_score false" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score)"/> 259 <option value="linear">linear</option>
135 <param name="param_use_rt_score" type="boolean" truevalue="-algorithm:Scores:use_rt_score true" falsevalue="-algorithm:Scores:use_rt_score false" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score)"/> 260 <option value="b_spline">b_spline</option>
136 <param name="param_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score true" falsevalue="-algorithm:Scores:use_library_score false" checked="true" optional="True" label="Use the library score" help="(-use_library_score)"/> 261 <option value="interpolated">interpolated</option>
137 <param name="param_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score true" falsevalue="-algorithm:Scores:use_elution_model_score false" checked="true" optional="True" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score)"/> 262 </param>
138 <param name="param_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score true" falsevalue="-algorithm:Scores:use_intensity_score false" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score)"/> 263 <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/>
139 <param name="param_use_nr_peaks_score" type="boolean" truevalue="-algorithm:Scores:use_nr_peaks_score true" falsevalue="-algorithm:Scores:use_nr_peaks_score false" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score)"/> 264 <param help="(-quantification_cutoff) " label="Cutoff in m/z below which peaks should not be used for quantification any more" min="0.0" name="param_algorithm_quantification_cutoff" optional="True" type="float" value="0.0"/>
140 <param name="param_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score true" falsevalue="-algorithm:Scores:use_total_xic_score false" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score)"/> 265 <param checked="false" falsevalue="" help="(-write_convex_hull) " label="Whether to write out all points of all features into the featureXML" name="param_algorithm_write_convex_hull" optional="True" truevalue="-algorithm:write_convex_hull" type="boolean"/>
141 <param name="param_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score true" falsevalue="-algorithm:Scores:use_sn_score false" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score)"/> 266 <param help="(-add_up_spectra) " label="Add up spectra around the peak apex (needs to be a non-even integer)" min="1" name="param_algorithm_add_up_spectra" optional="True" type="integer" value="1"/>
142 <param name="param_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores true" falsevalue="-algorithm:Scores:use_dia_scores false" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores)"/> 267 <param help="(-spacing_for_spectra_resampling) " label="If spectra are to be added, use this spacing to add them up" min="0.0" name="param_algorithm_spacing_for_spectra_resampling" optional="True" type="float" value="0.005"/>
143 <param name="param_use_ms1_correlation" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation true" falsevalue="-algorithm:Scores:use_ms1_correlation false" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation)"/> 268 <param help="(-min_peak_width) " label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0"/>
144 <param name="param_use_ms1_fullscan" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan true" falsevalue="-algorithm:Scores:use_ms1_fullscan false" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan)"/> 269 <param help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that" label="Try to apply a background subtraction to the peak (experimental)" name="param_algorithm_TransitionGroupPicker_background_subtraction" optional="True" type="select" value="none">
145 </expand> 270 <option value="none">none</option>
146 </inputs> 271 <option value="smoothed">smoothed</option>
147 <outputs> 272 <option value="original">original</option>
148 <data name="param_out" label="output file" format="featureXML"/> 273 </param>
149 </outputs> 274 <param help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" name="param_algorithm_TransitionGroupPicker_recalculate_peaks" size="30" type="text" value="false">
150 <help>**What it does** 275 <sanitizer>
151 276 <valid initial="string.printable">
152 Picks peaks and finds features in an SRM experiment. 277 <remove value="'"/>
278 <remove value="&quot;"/>
279 </valid>
280 </sanitizer>
281 </param>
282 <param help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0"/>
283 <param help="(-minimal_quality) " label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0"/>
284 <param 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" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" name="param_algorithm_TransitionGroupPicker_compute_peak_quality" size="30" type="text" value="false">
285 <sanitizer>
286 <valid initial="string.printable">
287 <remove value="'"/>
288 <remove value="&quot;"/>
289 </valid>
290 </sanitizer>
291 </param>
292 <param help="(-interpolation_step) " label="Sampling rate for the interpolation of the model function" name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2"/>
293 <param help="(-tolerance_stdev_bounding_box) " label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0"/>
294 <param help="(-max_iteration) " label="Maximum number of iterations using by Levenberg-Marquardt algorithm" name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500"/>
295 <param help="(-mean) " label="Centroid position of the model" name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0"/>
296 <param help="(-variance) " label="Variance of the model" name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0"/>
297 <param checked="true" falsevalue="" help="(-use_shape_score) " label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_shape_score" optional="True" truevalue="-algorithm:Scores:use_shape_score" type="boolean"/>
298 <param checked="true" falsevalue="" help="(-use_coelution_score) " label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_coelution_score" optional="True" truevalue="-algorithm:Scores:use_coelution_score" type="boolean"/>
299 <param checked="true" falsevalue="" help="(-use_rt_score) " label="Use the retention time score (this score measure the difference in retention time)" name="param_algorithm_Scores_use_rt_score" optional="True" truevalue="-algorithm:Scores:use_rt_score" type="boolean"/>
300 <param checked="true" falsevalue="" help="(-use_library_score) " label="Use the library score" name="param_algorithm_Scores_use_library_score" optional="True" truevalue="-algorithm:Scores:use_library_score" type="boolean"/>
301 <param checked="true" falsevalue="" help="(-use_elution_model_score) " label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" name="param_algorithm_Scores_use_elution_model_score" optional="True" truevalue="-algorithm:Scores:use_elution_model_score" type="boolean"/>
302 <param checked="true" falsevalue="" help="(-use_intensity_score) " label="Use the intensity score" name="param_algorithm_Scores_use_intensity_score" optional="True" truevalue="-algorithm:Scores:use_intensity_score" type="boolean"/>
303 <param checked="true" falsevalue="" help="(-use_nr_peaks_score) " label="Use the number of peaks score" name="param_algorithm_Scores_use_nr_peaks_score" optional="True" truevalue="-algorithm:Scores:use_nr_peaks_score" type="boolean"/>
304 <param checked="true" falsevalue="" help="(-use_total_xic_score) " label="Use the total XIC score" name="param_algorithm_Scores_use_total_xic_score" optional="True" truevalue="-algorithm:Scores:use_total_xic_score" type="boolean"/>
305 <param checked="true" falsevalue="" help="(-use_sn_score) " label="Use the SN (signal to noise) score" name="param_algorithm_Scores_use_sn_score" optional="True" truevalue="-algorithm:Scores:use_sn_score" type="boolean"/>
306 <param checked="true" falsevalue="" help="(-use_dia_scores) " label="Use the DIA (SWATH) scores" name="param_algorithm_Scores_use_dia_scores" optional="True" truevalue="-algorithm:Scores:use_dia_scores" type="boolean"/>
307 <param checked="false" falsevalue="" help="(-use_ms1_correlation) " label="Use the correlation scores with the MS1 elution profiles" name="param_algorithm_Scores_use_ms1_correlation" optional="True" truevalue="-algorithm:Scores:use_ms1_correlation" type="boolean"/>
308 <param checked="false" falsevalue="" help="(-use_ms1_fullscan) " label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" name="param_algorithm_Scores_use_ms1_fullscan" optional="True" truevalue="-algorithm:Scores:use_ms1_fullscan" type="boolean"/>
309 </expand>
310 </inputs>
311 <outputs>
312 <data format="xml" name="param_out"/>
313 </outputs>
314 <help>Picks peaks and finds features in an SRM experiment.
153 315
154 316
155 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html 317 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help>
156 318 </tool>
157 @REFERENCES@
158 </help>
159 </tool>