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comparison FeatureFinderCentroided.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.0.0">
3 <description>Detects two-dimensional features in LC-MS data.</description>
4 <macros>
5 <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>FeatureFinderCentroided
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_seeds:
19 -seeds $param_seeds
20 #end if
21 #if $param_out_mzq:
22 -out_mzq $param_out_mzq
23 #end if
24 -threads \${GALAXY_SLOTS:-24}
25 #if $param_algorithm_intensity_bins:
26 -algorithm:intensity:bins $param_algorithm_intensity_bins
27 #end if
28 #if $param_algorithm_mass_trace_mz_tolerance:
29 -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance
30 #end if
31 #if $param_algorithm_mass_trace_min_spectra:
32 -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra
33 #end if
34 #if $param_algorithm_mass_trace_max_missing:
35 -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing
36 #end if
37 #if $param_algorithm_mass_trace_slope_bound:
38 -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound
39 #end if
40 #if $param_algorithm_isotopic_pattern_charge_low:
41 -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low
42 #end if
43 #if $param_algorithm_isotopic_pattern_charge_high:
44 -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high
45 #end if
46 #if $param_algorithm_isotopic_pattern_mz_tolerance:
47 -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance
48 #end if
49 #if $param_algorithm_seed_min_score:
50 -algorithm:seed:min_score $param_algorithm_seed_min_score
51 #end if
52 #if $param_algorithm_feature_min_score:
53 -algorithm:feature:min_score $param_algorithm_feature_min_score
54 #end if
55 #if $param_algorithm_feature_reported_mz:
56 -algorithm:feature:reported_mz
57 #if " " in str($param_algorithm_feature_reported_mz):
58 "$param_algorithm_feature_reported_mz"
59 #else
60 $param_algorithm_feature_reported_mz
61 #end if
62 #end if
63 #if $param_algorithm_user_seed_rt_tolerance:
64 -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
65 #end if
66 #if $param_algorithm_user_seed_mz_tolerance:
67 -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance
68 #end if
69 #if $param_algorithm_user_seed_min_score:
70 -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score
71 #end if
72 #if $adv_opts.adv_opts_selector=='advanced':
73 #if $adv_opts.param_force:
74 -force
75 #end if
76 #if $adv_opts.param_algorithm_debug_pseudo_rt_shift:
77 -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift
78 #end if
79 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage:
80 -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage
81 #end if
82 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional:
83 -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional
84 #end if
85 #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement:
86 -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement
87 #end if
88 #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width:
89 -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width
90 #end if
91 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C:
92 -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C
93 #end if
94 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N:
95 -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N
96 #end if
97 #if $adv_opts.param_algorithm_fit_max_iterations:
98 -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations
99 #end if
100 #if $adv_opts.param_algorithm_feature_min_isotope_fit:
101 -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit
102 #end if
103 #if $adv_opts.param_algorithm_feature_min_trace_score:
104 -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score
105 #end if
106 #if $adv_opts.param_algorithm_feature_min_rt_span:
107 -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span
108 #end if
109 #if $adv_opts.param_algorithm_feature_max_rt_span:
110 -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
111 #end if
112 #if $adv_opts.param_algorithm_feature_rt_shape:
113 -algorithm:feature:rt_shape
114 #if " " in str($adv_opts.param_algorithm_feature_rt_shape):
115 "$adv_opts.param_algorithm_feature_rt_shape"
116 #else
117 $adv_opts.param_algorithm_feature_rt_shape
118 #end if
119 #end if
120 #if $adv_opts.param_algorithm_feature_max_intersection:
121 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
122 #end if
123 #end if
124 </command>
125 <inputs>
126 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
127 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/>
128 <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. &lt;br&gt;This parameter should be decreased, if the algorithm is used on small regions of a map"/>
129 <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) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/>
130 <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) "/>
131 <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) &lt;br&gt;This parameter should be well below 'min_spectra'!"/>
132 <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) &lt;br&gt;This parameter is important to seperate overlapping elution peaks. &lt;br&gt;It should be increased if feature elution profiles fluctuate a lot"/>
133 <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) "/>
134 <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) "/>
135 <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) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/>
136 <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) &lt;br&gt;The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. &lt;br&gt;If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
137 <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) &lt;br&gt;The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
138 <param name="param_algorithm_feature_reported_mz" type="select" optional="True" value="monoisotopic" label="The mass type that is reported for features" help="(-reported_mz) &lt;br&gt;'maximum' returns the m/z value of the highest mass trace. &lt;br&gt;'average' returns the intensity-weighted average m/z value of all contained peaks. &lt;br&gt;'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
139 <option value="maximum">maximum</option>
140 <option value="average">average</option>
141 <option value="monoisotopic">monoisotopic</option>
142 </param>
143 <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) "/>
144 <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) "/>
145 <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"/>
146 <expand macro="advanced_options">
147 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
148 <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) "/>
149 <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) "/>
150 <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) "/>
151 <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) "/>
152 <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) "/>
153 <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"/>
154 <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"/>
155 <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) "/>
156 <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) "/>
157 <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) &lt;br&gt;Traces below this threshold are removed after the model fitting. &lt;br&gt;This parameter is important for features that overlap in m/z dimension"/>
158 <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) "/>
159 <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) "/>
160 <param name="param_algorithm_feature_rt_shape" type="select" optional="True" 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">
161 <option value="symmetric">symmetric</option>
162 <option value="asymmetric">asymmetric</option>
163 </param>
164 <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) "/>
165 </expand>
166 </inputs>
167 <outputs>
168 <data name="param_out" format="featurexml"/>
169 <data name="param_out_mzq" format="mzq"/>
170 </outputs>
171 <help>**What it does**
172
173 Detects two-dimensional features in LC-MS data.
174
175
176 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help>
177 <expand macro="references"/>
178 </tool>