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comparison FeatureFinderMetaboIdent.xml @ 5:a93b05cf3a38 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:15 +0000
parents ae20e8a6d309
children
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equal deleted inserted replaced
4:ae20e8a6d309 5:a93b05cf3a38
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.--> 1 <!--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: [Utilities]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Detects features in MS1 data based on metabolite identifications.</description> 4 <description>Detects features in MS1 data based on metabolite identifications</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token> 6 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir id && 18 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && 19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 mkdir out && 20 mkdir out &&
22 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 21 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir lib_out && 22 mkdir lib_out &&
24 #end if 23 #end if
25 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 24 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 mkdir chrom_out && 25 mkdir chrom_out &&
27 #end if 26 #end if
27 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir trafo_out &&
29 #end if
28 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 30 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 mkdir candidates_out && 31 mkdir candidates_out &&
30 #end if
31 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 mkdir trafo_out &&
33 #end if 32 #end if
34 33
35 ## Main program call 34 ## Main program call
36 35
37 set -o pipefail && 36 set -o pipefail &&
50 #end if 49 #end if
51 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 50 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
52 -chrom_out 51 -chrom_out
53 'chrom_out/output.${gxy2omsext("mzml")}' 52 'chrom_out/output.${gxy2omsext("mzml")}'
54 #end if 53 #end if
55 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
56 -candidates_out
57 'candidates_out/output.${gxy2omsext("featurexml")}'
58 #end if
59 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 54 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
60 -trafo_out 55 -trafo_out
61 'trafo_out/output.${gxy2omsext("trafoxml")}' 56 'trafo_out/output.${gxy2omsext("trafoxml")}'
57 #end if
58 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
59 -candidates_out
60 'candidates_out/output.${gxy2omsext("txt")}'
62 #end if 61 #end if
63 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 62 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
64 | tee '$stdout' 63 | tee '$stdout'
65 #end if 64 #end if
66 65
70 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out' 69 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
71 #end if 70 #end if
72 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 71 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
73 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out' 72 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
74 #end if 73 #end if
75 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
76 && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
77 #end if
78 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 74 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
79 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out' 75 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
76 #end if
77 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
78 && mv 'candidates_out/output.${gxy2omsext("txt")}' '$candidates_out'
80 #end if 79 #end if
81 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 80 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
82 && mv '@EXECUTABLE@.ctd' '$ctd_out' 81 && mv '@EXECUTABLE@.ctd' '$ctd_out'
83 #end if]]></command> 82 #end if]]></command>
84 <configfiles> 83 <configfiles>
85 <inputs name="args_json" data_style="paths"/> 84 <inputs name="args_json" data_style="paths"/>
86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 85 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
87 </configfiles> 86 </configfiles>
88 <inputs> 87 <inputs>
89 <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/> 88 <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
90 <param argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/> 89 <param argument="-id" type="data" format="tabular" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
91 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false"> 90 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
92 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/> 91 <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
93 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/> 92 <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
94 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/> 93 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
95 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/> 94 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
96 </section> 95 </section>
97 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false"> 96 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
98 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/> 97 <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
99 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/> 98 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
100 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/> 99 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
101 </section> 100 </section>
102 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false"> 101 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
103 <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help=""> 102 <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
104 <option value="symmetric" selected="true">symmetric</option> 103 <option value="symmetric" selected="true">symmetric</option>
105 <option value="asymmetric">asymmetric</option> 104 <option value="asymmetric">asymmetric</option>
106 <option value="none">none</option> 105 <option value="none">none</option>
107 <expand macro="list_string_san" name="type"/> 106 <expand macro="list_string_san" name="type"/>
108 </param> 107 </param>
109 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> 108 <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
110 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/> 109 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
111 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/> 110 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
112 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/> 111 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
113 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false"> 112 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
114 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/> 113 <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
115 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> 114 <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
116 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 115 <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
117 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 116 <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
118 </section> 117 </section>
119 </section> 118 </section>
120 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false"> 119 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
121 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/> 120 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
122 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/> 121 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
123 </section> 122 </section>
124 <expand macro="adv_opts_macro"> 123 <expand macro="adv_opts_macro">
125 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 124 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
126 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 125 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
127 <expand macro="list_string_san" name="test"/> 126 <expand macro="list_string_san" name="test"/>
128 </param> 127 </param>
129 </expand> 128 </expand>
130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 129 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
131 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option> 130 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
132 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option> 131 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
133 <option value="candidates_out_FLAG">candidates_out (Optional output file with feature candidates)</option>
134 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option> 132 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
133 <option value="candidates_out_FLAG">candidates_out (Optional output file: Feature candidates (before filtering and model fitting))</option>
135 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 134 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
136 </param> 135 </param>
137 </inputs> 136 </inputs>
138 <outputs> 137 <outputs>
139 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> 138 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
141 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter> 140 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
142 </data> 141 </data>
143 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml"> 142 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
144 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter> 143 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
145 </data> 144 </data>
146 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
147 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
148 </data>
149 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml"> 145 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
150 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter> 146 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data> 147 </data>
148 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="txt">
149 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
150 </data>
152 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 151 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
153 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 152 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
154 </data> 153 </data>
155 </outputs> 154 </outputs>
156 <tests><!-- UTILS_FeatureFinderMetaboIdent_1 --> 155 <tests>
156 <!-- TOPP_FeatureFinderMetaboIdent_1 -->
157 <test expect_num_outputs="2"> 157 <test expect_num_outputs="2">
158 <section name="adv_opts"> 158 <section name="adv_opts">
159 <param name="force" value="false"/> 159 <param name="force" value="false"/>
160 <param name="test" value="true"/> 160 <param name="test" value="true"/>
161 </section> 161 </section>
162 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> 162 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
163 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> 163 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
164 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 164 <output name="out" value="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
165 <section name="extract"> 165 <section name="extract">
166 <param name="mz_window" value="5.0"/> 166 <param name="mz_window" value="5.0"/>
167 <param name="rt_window" value="20.0"/> 167 <param name="rt_window" value="20.0"/>
168 <param name="n_isotopes" value="2"/> 168 <param name="n_isotopes" value="2"/>
169 <param name="isotope_pmin" value="0.0"/> 169 <param name="isotope_pmin" value="0.0"/>
194 <output name="ctd_out" ftype="xml"> 194 <output name="ctd_out" ftype="xml">
195 <assert_contents> 195 <assert_contents>
196 <is_valid_xml/> 196 <is_valid_xml/>
197 </assert_contents> 197 </assert_contents>
198 </output> 198 </output>
199 <assert_stdout>
200 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
201 </assert_stdout>
199 </test> 202 </test>
200 </tests> 203 </tests>
201 <help><![CDATA[Detects features in MS1 data based on metabolite identifications. 204 <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
202 205
203 206
204 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help> 207 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetaboIdent.html]]></help>
205 <expand macro="references"/> 208 <expand macro="references"/>
206 </tool> 209 </tool>