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comparison FeatureFinderMetabo.xml @ 15:2451315543f9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:24:19 +0000
parents 00080bb4299e
children a49dde5a836e
comparison
equal deleted inserted replaced
14:55ebdf4618df 15:2451315543f9
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="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token> 7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
52 <configfiles> 50 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 51 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 53 </configfiles>
56 <inputs> 54 <inputs>
57 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> 55 <param argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/>
58 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 56 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
59 <section name="common" title="Common parameters for all other subsections" help="" expanded="false"> 57 <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
60 <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=""/> 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=""/>
61 <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=""/> 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=""/>
62 <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" 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=""/>
63 </section> 61 </section>
64 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false"> 62 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
65 <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=""/> 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=""/>
66 <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=""/> 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=""/>
67 <param name="quant_method" argument="-algorithm:mtd:quant_method" display="radio" type="select" optional="false" 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"> 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">
68 <option value="area" selected="true">area</option> 66 <option value="area" selected="true">area</option>
69 <option value="median">median</option> 67 <option value="median">median</option>
70 <option value="max_height">max_height</option> 68 <option value="max_height">max_height</option>
71 <expand macro="list_string_san"/> 69 <expand macro="list_string_san" name="quant_method"/>
72 </param> 70 </param>
73 <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" display="radio" type="select" optional="false" 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"> 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">
74 <option value="outlier" selected="true">outlier</option> 72 <option value="outlier" selected="true">outlier</option>
75 <option value="sample_rate">sample_rate</option> 73 <option value="sample_rate">sample_rate</option>
76 <expand macro="list_string_san"/> 74 <expand macro="list_string_san" name="trace_termination_criterion"/>
77 </param> 75 </param>
78 <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=""/> 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=""/>
79 <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=""/> 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=""/>
80 <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=""/> 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=""/>
81 <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"/> 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"/>
82 </section> 80 </section>
83 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false"> 81 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
84 <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"/> 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"/>
85 <param name="width_filtering" argument="-algorithm:epd:width_filtering" display="radio" type="select" optional="false" 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"> 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">
86 <option value="off">off</option> 84 <option value="off">off</option>
87 <option value="fixed" selected="true">fixed</option> 85 <option value="fixed" selected="true">fixed</option>
88 <option value="auto">auto</option> 86 <option value="auto">auto</option>
89 <expand macro="list_string_san"/> 87 <expand macro="list_string_san" name="width_filtering"/>
90 </param> 88 </param>
91 <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"/> 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"/>
92 <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"/> 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"/>
93 <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=""/> 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=""/>
94 </section> 92 </section>
97 <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=""/> 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=""/>
98 <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" 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=""/>
99 <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest 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=""/>
100 <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=""/> 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=""/>
101 <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"/> 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"/>
102 <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" display="radio" type="select" optional="false" 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"> 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">
103 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> 101 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
104 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> 102 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
105 <option value="peptides">peptides</option> 103 <option value="peptides">peptides</option>
106 <option value="none">none</option> 104 <option value="none">none</option>
107 <expand macro="list_string_san"/> 105 <expand macro="list_string_san" name="isotope_filtering_model"/>
108 </param> 106 </param>
109 <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.)"/> 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.)"/>
110 <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=""/> 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=""/>
111 <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=""/> 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=""/>
112 <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=""/> 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=""/>
113 <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'"/> 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'"/>
114 <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=""> 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="">
115 <expand macro="list_string_san"/> 113 <expand macro="list_string_san" name="elements"/>
116 </param> 114 </param>
117 </section> 115 </section>
118 </section> 116 </section>
119 <expand macro="adv_opts_macro"> 117 <expand macro="adv_opts_macro">
120 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 118 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
121 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 119 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
122 <expand macro="list_string_san"/> 120 <expand macro="list_string_san" name="test"/>
123 </param> 121 </param>
124 </expand> 122 </expand>
125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 123 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
126 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option> 124 <option value="out_chrom_FLAG">out_chrom (Optional mzML file with chromatograms)</option>
127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
134 </data> 132 </data>
135 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 133 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
136 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 134 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
137 </data> 135 </data>
138 </outputs> 136 </outputs>
139 <tests> 137 <tests><!-- TOPP_FeatureFinderMetabo_1 -->
140 <expand macro="autotest_FeatureFinderMetabo"/> 138 <test expect_num_outputs="2">
141 <expand macro="manutest_FeatureFinderMetabo"/> 139 <section name="adv_opts">
140 <param name="force" value="false"/>
141 <param name="test" value="true"/>
142 </section>
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"/>
145 <section name="algorithm">
146 <section name="common">
147 <param name="noise_threshold_int" value="10.0"/>
148 <param name="chrom_peak_snr" value="3.0"/>
149 <param name="chrom_fwhm" value="5.0"/>
150 </section>
151 <section name="mtd">
152 <param name="mass_error_ppm" value="20.0"/>
153 <param name="reestimate_mt_sd" value="true"/>
154 <param name="quant_method" value="area"/>
155 <param name="trace_termination_criterion" value="outlier"/>
156 <param name="trace_termination_outliers" value="5"/>
157 <param name="min_sample_rate" value="0.5"/>
158 <param name="min_trace_length" value="5.0"/>
159 <param name="max_trace_length" value="300.0"/>
160 </section>
161 <section name="epd">
162 <param name="enabled" value="true"/>
163 <param name="width_filtering" value="off"/>
164 <param name="min_fwhm" value="3.0"/>
165 <param name="max_fwhm" value="60.0"/>
166 <param name="masstrace_snr_filtering" value="false"/>
167 </section>
168 <section name="ffm">
169 <param name="local_rt_range" value="10.0"/>
170 <param name="local_mz_range" value="6.5"/>
171 <param name="charge_lower_bound" value="1"/>
172 <param name="charge_upper_bound" value="3"/>
173 <param name="report_summed_ints" value="false"/>
174 <param name="enable_RT_filtering" value="true"/>
175 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
176 <param name="mz_scoring_13C" value="true"/>
177 <param name="use_smoothed_intensities" value="true"/>
178 <param name="report_convex_hulls" value="false"/>
179 <param name="remove_single_traces" value="false"/>
180 <param name="mz_scoring_by_elements" value="false"/>
181 <param name="elements" value="CHNOPS"/>
182 </section>
183 </section>
184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
185 <output name="ctd_out" ftype="xml">
186 <assert_contents>
187 <is_valid_xml/>
188 </assert_contents>
189 </output>
190 </test>
191 <!-- TOPP_FeatureFinderMetabo_2 -->
192 <test expect_num_outputs="2">
193 <section name="adv_opts">
194 <param name="force" value="false"/>
195 <param name="test" value="true"/>
196 </section>
197 <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"/>
199 <section name="algorithm">
200 <section name="common">
201 <param name="noise_threshold_int" value="100.0"/>
202 <param name="chrom_peak_snr" value="0.0"/>
203 <param name="chrom_fwhm" value="100.0"/>
204 </section>
205 <section name="mtd">
206 <param name="mass_error_ppm" value="5.0"/>
207 <param name="reestimate_mt_sd" value="true"/>
208 <param name="quant_method" value="median"/>
209 <param name="trace_termination_criterion" value="sample_rate"/>
210 <param name="trace_termination_outliers" value="2"/>
211 <param name="min_sample_rate" value="0.01"/>
212 <param name="min_trace_length" value="30.0"/>
213 <param name="max_trace_length" value="3000.0"/>
214 </section>
215 <section name="epd">
216 <param name="enabled" value="false"/>
217 <param name="width_filtering" value="off"/>
218 <param name="min_fwhm" value="10.0"/>
219 <param name="max_fwhm" value="80.0"/>
220 <param name="masstrace_snr_filtering" value="false"/>
221 </section>
222 <section name="ffm">
223 <param name="local_rt_range" value="10.0"/>
224 <param name="local_mz_range" value="4.5"/>
225 <param name="charge_lower_bound" value="1"/>
226 <param name="charge_upper_bound" value="3"/>
227 <param name="report_summed_ints" value="false"/>
228 <param name="enable_RT_filtering" value="false"/>
229 <param name="isotope_filtering_model" value="none"/>
230 <param name="mz_scoring_13C" value="false"/>
231 <param name="use_smoothed_intensities" value="false"/>
232 <param name="report_convex_hulls" value="true"/>
233 <param name="remove_single_traces" value="false"/>
234 <param name="mz_scoring_by_elements" value="false"/>
235 <param name="elements" value="CHNOPS"/>
236 </section>
237 </section>
238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
239 <output name="ctd_out" ftype="xml">
240 <assert_contents>
241 <is_valid_xml/>
242 </assert_contents>
243 </output>
244 </test>
245 <!-- TOPP_FeatureFinderMetabo_3 -->
246 <test expect_num_outputs="3">
247 <section name="adv_opts">
248 <param name="force" value="false"/>
249 <param name="test" value="true"/>
250 </section>
251 <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"/>
253 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
254 <section name="algorithm">
255 <section name="common">
256 <param name="noise_threshold_int" value="10.0"/>
257 <param name="chrom_peak_snr" value="3.0"/>
258 <param name="chrom_fwhm" value="5.0"/>
259 </section>
260 <section name="mtd">
261 <param name="mass_error_ppm" value="5.0"/>
262 <param name="reestimate_mt_sd" value="true"/>
263 <param name="quant_method" value="area"/>
264 <param name="trace_termination_criterion" value="outlier"/>
265 <param name="trace_termination_outliers" value="5"/>
266 <param name="min_sample_rate" value="0.5"/>
267 <param name="min_trace_length" value="5.0"/>
268 <param name="max_trace_length" value="-1.0"/>
269 </section>
270 <section name="epd">
271 <param name="enabled" value="true"/>
272 <param name="width_filtering" value="fixed"/>
273 <param name="min_fwhm" value="3.0"/>
274 <param name="max_fwhm" value="60.0"/>
275 <param name="masstrace_snr_filtering" value="false"/>
276 </section>
277 <section name="ffm">
278 <param name="local_rt_range" value="10.0"/>
279 <param name="local_mz_range" value="6.5"/>
280 <param name="charge_lower_bound" value="1"/>
281 <param name="charge_upper_bound" value="3"/>
282 <param name="report_summed_ints" value="false"/>
283 <param name="enable_RT_filtering" value="true"/>
284 <param name="isotope_filtering_model" value="none"/>
285 <param name="mz_scoring_13C" value="true"/>
286 <param name="use_smoothed_intensities" value="true"/>
287 <param name="report_convex_hulls" value="true"/>
288 <param name="remove_single_traces" value="false"/>
289 <param name="mz_scoring_by_elements" value="false"/>
290 <param name="elements" value="CHNOPS"/>
291 </section>
292 </section>
293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
294 <output name="ctd_out" ftype="xml">
295 <assert_contents>
296 <is_valid_xml/>
297 </assert_contents>
298 </output>
299 </test>
300 <!-- TOPP_FeatureFinderMetabo_4 -->
301 <test expect_num_outputs="3">
302 <section name="adv_opts">
303 <param name="force" value="false"/>
304 <param name="test" value="true"/>
305 </section>
306 <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"/>
308 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
309 <section name="algorithm">
310 <section name="common">
311 <param name="noise_threshold_int" value="10.0"/>
312 <param name="chrom_peak_snr" value="3.0"/>
313 <param name="chrom_fwhm" value="5.0"/>
314 </section>
315 <section name="mtd">
316 <param name="mass_error_ppm" value="5.0"/>
317 <param name="reestimate_mt_sd" value="true"/>
318 <param name="quant_method" value="area"/>
319 <param name="trace_termination_criterion" value="outlier"/>
320 <param name="trace_termination_outliers" value="5"/>
321 <param name="min_sample_rate" value="0.5"/>
322 <param name="min_trace_length" value="5.0"/>
323 <param name="max_trace_length" value="-1.0"/>
324 </section>
325 <section name="epd">
326 <param name="enabled" value="true"/>
327 <param name="width_filtering" value="fixed"/>
328 <param name="min_fwhm" value="3.0"/>
329 <param name="max_fwhm" value="60.0"/>
330 <param name="masstrace_snr_filtering" value="false"/>
331 </section>
332 <section name="ffm">
333 <param name="local_rt_range" value="10.0"/>
334 <param name="local_mz_range" value="6.5"/>
335 <param name="charge_lower_bound" value="1"/>
336 <param name="charge_upper_bound" value="3"/>
337 <param name="report_summed_ints" value="false"/>
338 <param name="enable_RT_filtering" value="true"/>
339 <param name="isotope_filtering_model" value="none"/>
340 <param name="mz_scoring_13C" value="true"/>
341 <param name="use_smoothed_intensities" value="true"/>
342 <param name="report_convex_hulls" value="true"/>
343 <param name="remove_single_traces" value="true"/>
344 <param name="mz_scoring_by_elements" value="false"/>
345 <param name="elements" value="CHNOPS"/>
346 </section>
347 </section>
348 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
349 <output name="ctd_out" ftype="xml">
350 <assert_contents>
351 <is_valid_xml/>
352 </assert_contents>
353 </output>
354 </test>
355 <!-- TOPP_FeatureFinderMetabo_5 -->
356 <test expect_num_outputs="2">
357 <section name="adv_opts">
358 <param name="force" value="false"/>
359 <param name="test" value="true"/>
360 </section>
361 <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"/>
363 <section name="algorithm">
364 <section name="common">
365 <param name="noise_threshold_int" value="10.0"/>
366 <param name="chrom_peak_snr" value="3.0"/>
367 <param name="chrom_fwhm" value="5.0"/>
368 </section>
369 <section name="mtd">
370 <param name="mass_error_ppm" value="20.0"/>
371 <param name="reestimate_mt_sd" value="true"/>
372 <param name="quant_method" value="max_height"/>
373 <param name="trace_termination_criterion" value="outlier"/>
374 <param name="trace_termination_outliers" value="5"/>
375 <param name="min_sample_rate" value="0.5"/>
376 <param name="min_trace_length" value="5.0"/>
377 <param name="max_trace_length" value="300.0"/>
378 </section>
379 <section name="epd">
380 <param name="enabled" value="true"/>
381 <param name="width_filtering" value="off"/>
382 <param name="min_fwhm" value="3.0"/>
383 <param name="max_fwhm" value="60.0"/>
384 <param name="masstrace_snr_filtering" value="false"/>
385 </section>
386 <section name="ffm">
387 <param name="local_rt_range" value="10.0"/>
388 <param name="local_mz_range" value="6.5"/>
389 <param name="charge_lower_bound" value="1"/>
390 <param name="charge_upper_bound" value="3"/>
391 <param name="report_summed_ints" value="false"/>
392 <param name="enable_RT_filtering" value="true"/>
393 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
394 <param name="mz_scoring_13C" value="true"/>
395 <param name="use_smoothed_intensities" value="true"/>
396 <param name="report_convex_hulls" value="false"/>
397 <param name="remove_single_traces" value="false"/>
398 <param name="mz_scoring_by_elements" value="false"/>
399 <param name="elements" value="CHNOPS"/>
400 </section>
401 </section>
402 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
403 <output name="ctd_out" ftype="xml">
404 <assert_contents>
405 <is_valid_xml/>
406 </assert_contents>
407 </output>
408 </test>
142 </tests> 409 </tests>
143 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 410 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
144 411
145 412
146 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMetabo.html]]></help> 413 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help>
147 <expand macro="references"/> 414 <expand macro="references"/>
148 </tool> 415 </tool>