Mercurial > repos > galaxyp > openms_featurefindercentroided
comparison FeatureFinderCentroided.xml @ 11:6eda2adf7613 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:17:06 +0000 |
parents | c56b544a3fb2 |
children | b57f420a47b9 |
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10:d37f92333160 | 11:6eda2adf7613 |
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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 CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
4 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.3.0"> | 4 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Detects two-dimensional features in LC-MS data.</description> | 5 <description>Detects two-dimensional features in LC-MS data.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">FeatureFinderCentroided</token> | 7 <token name="@EXECUTABLE@">FeatureFinderCentroided</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[FeatureFinderCentroided | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
21 mkdir out && | |
22 #if $seeds: | |
23 mkdir seeds && | |
24 ln -s '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' && | |
17 #end if | 25 #end if |
18 #if $param_out: | 26 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
19 -out $param_out | 27 mkdir out_mzq && |
20 #end if | 28 #end if |
21 #if $param_seeds: | 29 |
22 -seeds $param_seeds | 30 ## Main program call |
31 | |
32 set -o pipefail && | |
33 @EXECUTABLE@ -write_ctd ./ && | |
34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
36 -in | |
37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
38 -out | |
39 'out/output.${gxy2omsext("featurexml")}' | |
40 #if $seeds: | |
41 -seeds | |
42 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' | |
23 #end if | 43 #end if |
24 #if $param_out_mzq: | 44 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
25 -out_mzq $param_out_mzq | 45 -out_mzq |
46 'out_mzq/output.${gxy2omsext("mzq")}' | |
26 #end if | 47 #end if |
27 #if $param_algorithm_intensity_bins: | 48 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
28 -algorithm:intensity:bins $param_algorithm_intensity_bins | 49 | tee '$stdout' |
29 #end if | 50 #end if |
30 #if $param_algorithm_mass_trace_mz_tolerance: | 51 |
31 -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance | 52 ## Postprocessing |
53 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' | |
54 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
55 && mv 'out_mzq/output.${gxy2omsext("mzq")}' '$out_mzq' | |
32 #end if | 56 #end if |
33 #if $param_algorithm_mass_trace_min_spectra: | 57 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
34 -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra | 58 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
35 #end if | 59 #end if]]></command> |
36 #if $param_algorithm_mass_trace_max_missing: | 60 <configfiles> |
37 -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing | 61 <inputs name="args_json" data_style="paths"/> |
38 #end if | 62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
39 #if $param_algorithm_mass_trace_slope_bound: | 63 </configfiles> |
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 $param_algorithm_feature_reported_mz: | |
58 -algorithm:feature:reported_mz | |
59 #if " " in str($param_algorithm_feature_reported_mz): | |
60 "$param_algorithm_feature_reported_mz" | |
61 #else | |
62 $param_algorithm_feature_reported_mz | |
63 #end if | |
64 #end if | |
65 #if $param_algorithm_user_seed_rt_tolerance: | |
66 -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance | |
67 #end if | |
68 #if $param_algorithm_user_seed_mz_tolerance: | |
69 -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance | |
70 #end if | |
71 #if $param_algorithm_user_seed_min_score: | |
72 -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score | |
73 #end if | |
74 #if $adv_opts.adv_opts_selector=='advanced': | |
75 #if $adv_opts.param_force: | |
76 -force | |
77 #end if | |
78 #if $adv_opts.param_algorithm_debug_pseudo_rt_shift: | |
79 -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift | |
80 #end if | |
81 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage: | |
82 -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage | |
83 #end if | |
84 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional: | |
85 -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional | |
86 #end if | |
87 #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement: | |
88 -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement | |
89 #end if | |
90 #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width: | |
91 -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width | |
92 #end if | |
93 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C: | |
94 -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C | |
95 #end if | |
96 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N: | |
97 -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N | |
98 #end if | |
99 #if $adv_opts.param_algorithm_fit_max_iterations: | |
100 -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations | |
101 #end if | |
102 #if $adv_opts.param_algorithm_feature_min_isotope_fit: | |
103 -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit | |
104 #end if | |
105 #if $adv_opts.param_algorithm_feature_min_trace_score: | |
106 -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score | |
107 #end if | |
108 #if $adv_opts.param_algorithm_feature_min_rt_span: | |
109 -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span | |
110 #end if | |
111 #if $adv_opts.param_algorithm_feature_max_rt_span: | |
112 -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span | |
113 #end if | |
114 #if $adv_opts.param_algorithm_feature_rt_shape: | |
115 -algorithm:feature:rt_shape | |
116 #if " " in str($adv_opts.param_algorithm_feature_rt_shape): | |
117 "$adv_opts.param_algorithm_feature_rt_shape" | |
118 #else | |
119 $adv_opts.param_algorithm_feature_rt_shape | |
120 #end if | |
121 #end if | |
122 #if $adv_opts.param_algorithm_feature_max_intersection: | |
123 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection | |
124 #end if | |
125 #end if | |
126 -threads "\${GALAXY_SLOTS:-1}" | |
127 ]]></command> | |
128 <inputs> | 64 <inputs> |
129 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> | 65 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> |
130 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/> | 66 <param name="seeds" argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/> |
131 <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"/> | 67 <section name="algorithm" title="Algorithm section" help="" expanded="false"> |
132 <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!"/> | 68 <section name="debug" title="" help="" expanded="false"> |
133 <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) "/> | 69 <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" optional="true" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/> |
134 <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'!"/> | 70 </section> |
135 <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"/> | 71 <section name="intensity" title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)" help="" expanded="false"> |
136 <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) "/> | 72 <param name="bins" argument="-algorithm:intensity:bins" type="integer" optional="true" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/> |
137 <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) "/> | 73 </section> |
138 <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!"/> | 74 <section name="mass_trace" title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)" help="" expanded="false"> |
139 <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"/> | 75 <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/> |
140 <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"/> | 76 <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" optional="true" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/> |
141 <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"> | 77 <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" optional="true" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/> |
142 <option value="maximum">maximum</option> | 78 <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to seperate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/> |
143 <option value="average">average</option> | 79 </section> |
144 <option value="monoisotopic" selected="true">monoisotopic</option> | 80 <section name="isotopic_pattern" title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)" help="" expanded="false"> |
81 <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" optional="true" min="1" value="1" label="Lowest charge to search fo" help=""/> | |
82 <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" optional="true" min="1" value="4" label="Highest charge to search fo" help=""/> | |
83 <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/> | |
84 <param name="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" optional="true" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/> | |
85 <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" optional="true" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/> | |
86 <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" optional="true" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/> | |
87 <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" optional="true" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/> | |
88 <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" optional="true" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/> | |
89 <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" optional="true" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/> | |
90 </section> | |
91 <section name="seed" title="Settings that determine which peaks are considered a seed" help="" expanded="false"> | |
92 <param name="min_score" argument="-algorithm:seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/> | |
93 </section> | |
94 <section name="fit" title="Settings for the model fitting" help="" expanded="false"> | |
95 <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" optional="true" min="1" value="500" label="Maximum number of iterations of the fit" help=""/> | |
96 </section> | |
97 <section name="feature" title="Settings for the features (intensity, quality assessment, ...)" help="" expanded="false"> | |
98 <param name="min_score" argument="-algorithm:feature:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/> | |
99 <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/> | |
100 <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/> | |
101 <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="true" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/> | |
102 <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="true" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/> | |
103 <param name="rt_shape" argument="-algorithm:feature:rt_shape" display="radio" type="select" optional="false" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used"> | |
104 <option value="symmetric" selected="true">symmetric</option> | |
105 <option value="asymmetric">asymmetric</option> | |
106 <expand macro="list_string_san"/> | |
107 </param> | |
108 <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="true" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/> | |
109 <param name="reported_mz" argument="-algorithm:feature:reported_mz" display="radio" type="select" optional="false" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model"> | |
110 <option value="maximum">maximum</option> | |
111 <option value="average">average</option> | |
112 <option value="monoisotopic" selected="true">monoisotopic</option> | |
113 <expand macro="list_string_san"/> | |
114 </param> | |
115 </section> | |
116 <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false"> | |
117 <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/> | |
118 <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" optional="true" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/> | |
119 <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/> | |
120 </section> | |
121 </section> | |
122 <expand macro="adv_opts_macro"> | |
123 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
124 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
125 <expand macro="list_string_san"/> | |
126 </param> | |
127 </expand> | |
128 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
129 <option value="out_mzq_FLAG">out_mzq (Overwrites 'seed:min_score' for user-specified seeds)</option> | |
130 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
145 </param> | 131 </param> |
146 <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) "/> | |
147 <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) "/> | |
148 <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"/> | |
149 <expand macro="advanced_options"> | |
150 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
151 <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) "/> | |
152 <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) "/> | |
153 <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) "/> | |
154 <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) "/> | |
155 <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) "/> | |
156 <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"/> | |
157 <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"/> | |
158 <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) "/> | |
159 <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) "/> | |
160 <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"/> | |
161 <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) "/> | |
162 <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) "/> | |
163 <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"> | |
164 <option value="symmetric" selected="true">symmetric</option> | |
165 <option value="asymmetric">asymmetric</option> | |
166 </param> | |
167 <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) "/> | |
168 </expand> | |
169 </inputs> | 132 </inputs> |
170 <outputs> | 133 <outputs> |
171 <data name="param_out" format="featurexml"/> | 134 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
172 <data name="param_out_mzq" format="mzq"/> | 135 <data name="out_mzq" label="${tool.name} on ${on_string}: out_mzq" format="mzq"> |
136 <filter>OPTIONAL_OUTPUTS is not None and "out_mzq_FLAG" in OPTIONAL_OUTPUTS</filter> | |
137 </data> | |
138 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
139 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
140 </data> | |
173 </outputs> | 141 </outputs> |
174 <help>Detects two-dimensional features in LC-MS data. | 142 <tests> |
143 <expand macro="autotest_FeatureFinderCentroided"/> | |
144 <expand macro="manutest_FeatureFinderCentroided"/> | |
145 </tests> | |
146 <help><![CDATA[Detects two-dimensional features in LC-MS data. | |
175 | 147 |
176 | 148 |
177 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderCentroided.html</help> | 149 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderCentroided.html]]></help> |
150 <expand macro="references"/> | |
178 </tool> | 151 </tool> |