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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 21:42:49 +0000
parents 2451315543f9
children
comparison
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15:2451315543f9 16:a49dde5a836e
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: [Quantitation]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description> 4 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token> 6 <token name="@EXECUTABLE@">FeatureFinderMetabo</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($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir out_chrom && 20 mkdir out_chrom &&
22 #end if 21 #end if
23 22
50 <configfiles> 49 <configfiles>
51 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
53 </configfiles> 52 </configfiles>
54 <inputs> 53 <inputs>
55 <param argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> 54 <param argument="-in" type="data" format="mzml" label="Centroided mzML file" help=" select mzml data sets(s)"/>
56 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
57 <section name="common" title="Common parameters for all other subsections" help="" expanded="false"> 56 <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
58 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/> 57 <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
59 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/> 58 <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
60 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/> 59 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
61 </section> 60 </section>
62 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false"> 61 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
63 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/> 62 <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
64 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/> 63 <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
65 <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace"> 64 <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
66 <option value="area" selected="true">area</option> 65 <option value="area" selected="true">area</option>
67 <option value="median">median</option> 66 <option value="median">median</option>
68 <option value="max_height">max_height</option> 67 <option value="max_height">max_height</option>
69 <expand macro="list_string_san" name="quant_method"/> 68 <expand macro="list_string_san" name="quant_method"/>
70 </param> 69 </param>
71 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold"> 70 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
72 <option value="outlier" selected="true">outlier</option> 71 <option value="outlier" selected="true">outlier</option>
73 <option value="sample_rate">sample_rate</option> 72 <option value="sample_rate">sample_rate</option>
74 <expand macro="list_string_san" name="trace_termination_criterion"/> 73 <expand macro="list_string_san" name="trace_termination_criterion"/>
75 </param> 74 </param>
76 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/> 75 <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
77 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/> 76 <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
78 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/> 77 <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
79 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/> 78 <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
80 </section> 79 </section>
81 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false"> 80 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
82 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/> 81 <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
83 <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution"> 82 <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
84 <option value="off">off</option> 83 <option value="off">off</option>
85 <option value="fixed" selected="true">fixed</option> 84 <option value="fixed" selected="true">fixed</option>
86 <option value="auto">auto</option> 85 <option value="auto">auto</option>
87 <expand macro="list_string_san" name="width_filtering"/> 86 <expand macro="list_string_san" name="width_filtering"/>
88 </param> 87 </param>
89 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 88 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
90 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> 89 <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
91 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/> 90 <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
92 </section> 91 </section>
93 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false"> 92 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
94 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/> 93 <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
95 <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/> 94 <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
96 <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/> 95 <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help=""/>
97 <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/> 96 <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help=""/>
98 <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/> 97 <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
99 <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/> 98 <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
100 <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="true" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device"> 99 <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
101 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> 100 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
102 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> 101 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
103 <option value="peptides">peptides</option> 102 <option value="peptides">peptides</option>
104 <option value="none">none</option> 103 <option value="none">none</option>
105 <expand macro="list_string_san" name="isotope_filtering_model"/> 104 <expand macro="list_string_san" name="isotope_filtering_model"/>
107 <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/> 106 <param name="mz_scoring_13C" argument="-algorithm:ffm:mz_scoring_13C" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
108 <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/> 107 <param name="use_smoothed_intensities" argument="-algorithm:ffm:use_smoothed_intensities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use LOWESS intensities instead of raw intensities" help=""/>
109 <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/> 108 <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/>
110 <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/> 109 <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/>
111 <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/> 110 <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/>
112 <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help=""> 111 <param name="elements" argument="-algorithm:ffm:elements" type="text" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
113 <expand macro="list_string_san" name="elements"/> 112 <expand macro="list_string_san" name="elements"/>
114 </param> 113 </param>
115 </section> 114 </section>
116 </section> 115 </section>
117 <expand macro="adv_opts_macro"> 116 <expand macro="adv_opts_macro">
118 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 117 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
119 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 118 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
120 <expand macro="list_string_san" name="test"/> 119 <expand macro="list_string_san" name="test"/>
121 </param> 120 </param>
122 </expand> 121 </expand>
123 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 122 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
124 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option> 123 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option>
132 </data> 131 </data>
133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
135 </data> 134 </data>
136 </outputs> 135 </outputs>
137 <tests><!-- TOPP_FeatureFinderMetabo_1 --> 136 <tests>
137 <!-- TOPP_FeatureFinderMetabo_1 -->
138 <test expect_num_outputs="2"> 138 <test expect_num_outputs="2">
139 <section name="adv_opts"> 139 <section name="adv_opts">
140 <param name="force" value="false"/> 140 <param name="force" value="false"/>
141 <param name="test" value="true"/> 141 <param name="test" value="true"/>
142 </section> 142 </section>
143 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> 143 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
144 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 144 <output name="out" value="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
145 <section name="algorithm"> 145 <section name="algorithm">
146 <section name="common"> 146 <section name="common">
147 <param name="noise_threshold_int" value="10.0"/> 147 <param name="noise_threshold_int" value="10.0"/>
148 <param name="chrom_peak_snr" value="3.0"/> 148 <param name="chrom_peak_snr" value="3.0"/>
149 <param name="chrom_fwhm" value="5.0"/> 149 <param name="chrom_fwhm" value="5.0"/>
185 <output name="ctd_out" ftype="xml"> 185 <output name="ctd_out" ftype="xml">
186 <assert_contents> 186 <assert_contents>
187 <is_valid_xml/> 187 <is_valid_xml/>
188 </assert_contents> 188 </assert_contents>
189 </output> 189 </output>
190 <assert_stdout>
191 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
192 </assert_stdout>
190 </test> 193 </test>
191 <!-- TOPP_FeatureFinderMetabo_2 --> 194 <!-- TOPP_FeatureFinderMetabo_2 -->
192 <test expect_num_outputs="2"> 195 <test expect_num_outputs="2">
193 <section name="adv_opts"> 196 <section name="adv_opts">
194 <param name="force" value="false"/> 197 <param name="force" value="false"/>
195 <param name="test" value="true"/> 198 <param name="test" value="true"/>
196 </section> 199 </section>
197 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> 200 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
198 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 201 <output name="out" value="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
199 <section name="algorithm"> 202 <section name="algorithm">
200 <section name="common"> 203 <section name="common">
201 <param name="noise_threshold_int" value="100.0"/> 204 <param name="noise_threshold_int" value="100.0"/>
202 <param name="chrom_peak_snr" value="0.0"/> 205 <param name="chrom_peak_snr" value="0.0"/>
203 <param name="chrom_fwhm" value="100.0"/> 206 <param name="chrom_fwhm" value="100.0"/>
239 <output name="ctd_out" ftype="xml"> 242 <output name="ctd_out" ftype="xml">
240 <assert_contents> 243 <assert_contents>
241 <is_valid_xml/> 244 <is_valid_xml/>
242 </assert_contents> 245 </assert_contents>
243 </output> 246 </output>
247 <assert_stdout>
248 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
249 </assert_stdout>
244 </test> 250 </test>
245 <!-- TOPP_FeatureFinderMetabo_3 --> 251 <!-- TOPP_FeatureFinderMetabo_3 -->
246 <test expect_num_outputs="3"> 252 <test expect_num_outputs="3">
247 <section name="adv_opts"> 253 <section name="adv_opts">
248 <param name="force" value="false"/> 254 <param name="force" value="false"/>
249 <param name="test" value="true"/> 255 <param name="test" value="true"/>
250 </section> 256 </section>
251 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> 257 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
252 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 258 <output name="out" value="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
253 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 259 <output name="out_chrom" value="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
254 <section name="algorithm"> 260 <section name="algorithm">
255 <section name="common"> 261 <section name="common">
256 <param name="noise_threshold_int" value="10.0"/> 262 <param name="noise_threshold_int" value="10.0"/>
257 <param name="chrom_peak_snr" value="3.0"/> 263 <param name="chrom_peak_snr" value="3.0"/>
258 <param name="chrom_fwhm" value="5.0"/> 264 <param name="chrom_fwhm" value="5.0"/>
294 <output name="ctd_out" ftype="xml"> 300 <output name="ctd_out" ftype="xml">
295 <assert_contents> 301 <assert_contents>
296 <is_valid_xml/> 302 <is_valid_xml/>
297 </assert_contents> 303 </assert_contents>
298 </output> 304 </output>
305 <assert_stdout>
306 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
307 </assert_stdout>
299 </test> 308 </test>
300 <!-- TOPP_FeatureFinderMetabo_4 --> 309 <!-- TOPP_FeatureFinderMetabo_4 -->
301 <test expect_num_outputs="3"> 310 <test expect_num_outputs="3">
302 <section name="adv_opts"> 311 <section name="adv_opts">
303 <param name="force" value="false"/> 312 <param name="force" value="false"/>
304 <param name="test" value="true"/> 313 <param name="test" value="true"/>
305 </section> 314 </section>
306 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> 315 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
307 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 316 <output name="out" value="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
308 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 317 <output name="out_chrom" value="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
309 <section name="algorithm"> 318 <section name="algorithm">
310 <section name="common"> 319 <section name="common">
311 <param name="noise_threshold_int" value="10.0"/> 320 <param name="noise_threshold_int" value="10.0"/>
312 <param name="chrom_peak_snr" value="3.0"/> 321 <param name="chrom_peak_snr" value="3.0"/>
313 <param name="chrom_fwhm" value="5.0"/> 322 <param name="chrom_fwhm" value="5.0"/>
349 <output name="ctd_out" ftype="xml"> 358 <output name="ctd_out" ftype="xml">
350 <assert_contents> 359 <assert_contents>
351 <is_valid_xml/> 360 <is_valid_xml/>
352 </assert_contents> 361 </assert_contents>
353 </output> 362 </output>
363 <assert_stdout>
364 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
365 </assert_stdout>
354 </test> 366 </test>
355 <!-- TOPP_FeatureFinderMetabo_5 --> 367 <!-- TOPP_FeatureFinderMetabo_5 -->
356 <test expect_num_outputs="2"> 368 <test expect_num_outputs="2">
357 <section name="adv_opts"> 369 <section name="adv_opts">
358 <param name="force" value="false"/> 370 <param name="force" value="false"/>
359 <param name="test" value="true"/> 371 <param name="test" value="true"/>
360 </section> 372 </section>
361 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> 373 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
362 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> 374 <output name="out" value="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
363 <section name="algorithm"> 375 <section name="algorithm">
364 <section name="common"> 376 <section name="common">
365 <param name="noise_threshold_int" value="10.0"/> 377 <param name="noise_threshold_int" value="10.0"/>
366 <param name="chrom_peak_snr" value="3.0"/> 378 <param name="chrom_peak_snr" value="3.0"/>
367 <param name="chrom_fwhm" value="5.0"/> 379 <param name="chrom_fwhm" value="5.0"/>
403 <output name="ctd_out" ftype="xml"> 415 <output name="ctd_out" ftype="xml">
404 <assert_contents> 416 <assert_contents>
405 <is_valid_xml/> 417 <is_valid_xml/>
406 </assert_contents> 418 </assert_contents>
407 </output> 419 </output>
420 <assert_stdout>
421 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
422 </assert_stdout>
408 </test> 423 </test>
409 </tests> 424 </tests>
410 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 425 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
411 426
412 427
413 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help> 428 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetabo.html]]></help>
414 <expand macro="references"/> 429 <expand macro="references"/>
415 </tool> 430 </tool>