Mercurial > repos > galaxyp > openms_featurefindercentroided
comparison FeatureFinderCentroided.xml @ 0:7dd3b4327a17 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:29:02 -0500 |
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children | 9e6a24fc4f4a |
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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: [Quantitation]--> | |
4 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.1.0"> | |
5 <description>Detects two-dimensional features in LC-MS data.</description> | |
6 <macros> | |
7 <token name="@EXECUTABLE@">FeatureFinderCentroided</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="references"/> | |
11 <expand macro="stdio"/> | |
12 <expand macro="requirements"/> | |
13 <command>FeatureFinderCentroided | |
14 | |
15 #if $param_in: | |
16 -in $param_in | |
17 #end if | |
18 #if $param_out: | |
19 -out $param_out | |
20 #end if | |
21 #if $param_seeds: | |
22 -seeds $param_seeds | |
23 #end if | |
24 #if $param_out_mzq: | |
25 -out_mzq $param_out_mzq | |
26 #end if | |
27 #if $param_algorithm_intensity_bins: | |
28 -algorithm:intensity:bins $param_algorithm_intensity_bins | |
29 #end if | |
30 #if $param_algorithm_mass_trace_mz_tolerance: | |
31 -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance | |
32 #end if | |
33 #if $param_algorithm_mass_trace_min_spectra: | |
34 -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra | |
35 #end if | |
36 #if $param_algorithm_mass_trace_max_missing: | |
37 -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing | |
38 #end if | |
39 #if $param_algorithm_mass_trace_slope_bound: | |
40 -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound | |
41 #end if | |
42 #if $param_algorithm_isotopic_pattern_charge_low: | |
43 -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low | |
44 #end if | |
45 #if $param_algorithm_isotopic_pattern_charge_high: | |
46 -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high | |
47 #end if | |
48 #if $param_algorithm_isotopic_pattern_mz_tolerance: | |
49 -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance | |
50 #end if | |
51 #if $param_algorithm_seed_min_score: | |
52 -algorithm:seed:min_score $param_algorithm_seed_min_score | |
53 #end if | |
54 #if $param_algorithm_feature_min_score: | |
55 -algorithm:feature:min_score $param_algorithm_feature_min_score | |
56 #end if | |
57 #if $param_algorithm_feature_reported_mz: | |
58 -algorithm:feature:reported_mz $param_algorithm_feature_reported_mz | |
59 #end if | |
60 #if $param_algorithm_user_seed_rt_tolerance: | |
61 -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance | |
62 #end if | |
63 #if $param_algorithm_user_seed_mz_tolerance: | |
64 -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance | |
65 #end if | |
66 #if $param_algorithm_user_seed_min_score: | |
67 -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score | |
68 #end if | |
69 #if $adv_opts.adv_opts_selector=='advanced': | |
70 #if $adv_opts.param_force: | |
71 -force | |
72 #end if | |
73 #if $adv_opts.param_algorithm_debug_pseudo_rt_shift: | |
74 -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift | |
75 #end if | |
76 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage: | |
77 -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage | |
78 #end if | |
79 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional: | |
80 -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional | |
81 #end if | |
82 #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement: | |
83 -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement | |
84 #end if | |
85 #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width: | |
86 -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width | |
87 #end if | |
88 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C: | |
89 -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C | |
90 #end if | |
91 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N: | |
92 -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N | |
93 #end if | |
94 #if $adv_opts.param_algorithm_fit_max_iterations: | |
95 -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations | |
96 #end if | |
97 #if $adv_opts.param_algorithm_feature_min_isotope_fit: | |
98 -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit | |
99 #end if | |
100 #if $adv_opts.param_algorithm_feature_min_trace_score: | |
101 -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score | |
102 #end if | |
103 #if $adv_opts.param_algorithm_feature_min_rt_span: | |
104 -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span | |
105 #end if | |
106 #if $adv_opts.param_algorithm_feature_max_rt_span: | |
107 -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span | |
108 #end if | |
109 #if $adv_opts.param_algorithm_feature_rt_shape: | |
110 -algorithm:feature:rt_shape $adv_opts.param_algorithm_feature_rt_shape | |
111 #end if | |
112 #if $adv_opts.param_algorithm_feature_max_intersection: | |
113 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection | |
114 #end if | |
115 #end if | |
116 </command> | |
117 <inputs> | |
118 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> | |
119 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/> | |
120 <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. <br>This parameter should be decreased, if the algorithm is used on small regions of a map"/> | |
121 <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/> | |
122 <param name="param_algorithm_mass_trace_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help="(-min_spectra) "/> | |
123 <param name="param_algorithm_mass_trace_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="(-max_missing) <br>This parameter should be well below 'min_spectra'!"/> | |
124 <param name="param_algorithm_mass_trace_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="(-slope_bound) <br>This parameter is important to seperate overlapping elution peaks. <br>It should be increased if feature elution profiles fluctuate a lot"/> | |
125 <param name="param_algorithm_isotopic_pattern_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search fo" help="(-charge_low) "/> | |
126 <param name="param_algorithm_isotopic_pattern_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search fo" help="(-charge_high) "/> | |
127 <param name="param_algorithm_isotopic_pattern_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/> | |
128 <param name="param_algorithm_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="(-min_score) <br>The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. <br>If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/> | |
129 <param name="param_algorithm_feature_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported" help="(-min_score) <br>The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/> | |
130 <param name="param_algorithm_feature_reported_mz" display="radio" type="select" optional="False" value="monoisotopic" label="The mass type that is reported for features" help="(-reported_mz) <br>'maximum' returns the m/z value of the highest mass trace. <br>'average' returns the intensity-weighted average m/z value of all contained peaks. <br>'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model"> | |
131 <option value="maximum">maximum</option> | |
132 <option value="average">average</option> | |
133 <option value="monoisotopic" selected="true">monoisotopic</option> | |
134 </param> | |
135 <param name="param_algorithm_user_seed_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help="(-rt_tolerance) "/> | |
136 <param name="param_algorithm_user_seed_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help="(-mz_tolerance) "/> | |
137 <param name="param_algorithm_user_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="(-min_score) The cutoff is typically a bit lower in this case"/> | |
138 <expand macro="advanced_options"> | |
139 <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_algorithm_debug_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when" help="(-pseudo_rt_shift) "/> | |
141 <param name="param_algorithm_isotopic_pattern_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help="(-intensity_percentage) "/> | |
142 <param name="param_algorithm_isotopic_pattern_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help="(-intensity_percentage_optional) "/> | |
143 <param name="param_algorithm_isotopic_pattern_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help="(-optional_fit_improvement) "/> | |
144 <param name="param_algorithm_isotopic_pattern_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help="(-mass_window_width) "/> | |
145 <param name="param_algorithm_isotopic_pattern_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel" help="(-abundance_12C) abundance of the light carbon. Modify if labeled"/> | |
146 <param name="param_algorithm_isotopic_pattern_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel" help="(-abundance_14N) abundance of the light nitrogen. Modify if labeled"/> | |
147 <param name="param_algorithm_fit_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit" help="(-max_iterations) "/> | |
148 <param name="param_algorithm_feature_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting" help="(-min_isotope_fit) "/> | |
149 <param name="param_algorithm_feature_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold" help="(-min_trace_score) <br>Traces below this threshold are removed after the model fitting. <br>This parameter is important for features that overlap in m/z dimension"/> | |
150 <param name="param_algorithm_feature_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help="(-min_rt_span) "/> | |
151 <param name="param_algorithm_feature_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help="(-max_rt_span) "/> | |
152 <param name="param_algorithm_feature_rt_shape" display="radio" type="select" optional="False" value="symmetric" label="Choose model used for RT profile fitting" help="(-rt_shape) If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used"> | |
153 <option value="symmetric" selected="true">symmetric</option> | |
154 <option value="asymmetric">asymmetric</option> | |
155 </param> | |
156 <param name="param_algorithm_feature_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features" help="(-max_intersection) "/> | |
157 </expand> | |
158 </inputs> | |
159 <outputs> | |
160 <data name="param_out" format="featurexml"/> | |
161 <data name="param_out_mzq" format="mzq"/> | |
162 </outputs> | |
163 <help>Detects two-dimensional features in LC-MS data. | |
164 | |
165 | |
166 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help> | |
167 </tool> |