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comparison FeatureFinderCentroided.xml @ 11:6eda2adf7613 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:17:06 +0000
parents c56b544a3fb2
children b57f420a47b9
comparison
equal deleted inserted replaced
10:d37f92333160 11:6eda2adf7613
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. &lt;br&gt;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) &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!"/> 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) &lt;br&gt;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) &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"/> 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) &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!"/> 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) &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"/> 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) &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"/> 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) &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"> 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) &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"/>
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>