Mercurial > repos > galaxyp > openms_featurefindermetabo
comparison FeatureFinderMetabo.xml @ 11:21dc135961b5 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 12:50:20 +0000 |
parents | b6e4da302f66 |
children | 00080bb4299e |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Quantitation]--> | 3 <!--Proposed Tool Section: [Quantitation]--> |
4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.3.0"> | 4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
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> | |
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[FeatureFinderMetabo | 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($in.ext)' && | |
21 mkdir out && | |
22 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
23 mkdir out_chrom && | |
17 #end if | 24 #end if |
18 #if $param_out: | 25 |
19 -out $param_out | 26 ## Main program call |
27 | |
28 set -o pipefail && | |
29 @EXECUTABLE@ -write_ctd ./ && | |
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
32 -in | |
33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
34 -out | |
35 'out/output.${gxy2omsext("featurexml")}' | |
36 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
37 -out_chrom | |
38 'out_chrom/output.${gxy2omsext("mzml")}' | |
20 #end if | 39 #end if |
21 #if $param_out_chrom: | 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
22 -out_chrom $param_out_chrom | 41 | tee '$stdout' |
23 #end if | 42 #end if |
24 #if $param_algorithm_common_noise_threshold_int: | 43 |
25 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int | 44 ## Postprocessing |
45 && mv 'out/output.${gxy2omsext("featurexml")}' '$out' | |
46 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
47 && mv 'out_chrom/output.${gxy2omsext("mzml")}' '$out_chrom' | |
26 #end if | 48 #end if |
27 #if $param_algorithm_common_chrom_peak_snr: | 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
28 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr | 50 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
29 #end if | 51 #end if]]></command> |
30 #if $param_algorithm_common_chrom_fwhm: | 52 <configfiles> |
31 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm | 53 <inputs name="args_json" data_style="paths"/> |
32 #end if | 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
33 #if $param_algorithm_mtd_mass_error_ppm: | 55 </configfiles> |
34 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm | |
35 #end if | |
36 #if $param_algorithm_mtd_reestimate_mt_sd: | |
37 -algorithm:mtd:reestimate_mt_sd | |
38 #if " " in str($param_algorithm_mtd_reestimate_mt_sd): | |
39 "$param_algorithm_mtd_reestimate_mt_sd" | |
40 #else | |
41 $param_algorithm_mtd_reestimate_mt_sd | |
42 #end if | |
43 #end if | |
44 #if $param_algorithm_mtd_quant_method: | |
45 -algorithm:mtd:quant_method | |
46 #if " " in str($param_algorithm_mtd_quant_method): | |
47 "$param_algorithm_mtd_quant_method" | |
48 #else | |
49 $param_algorithm_mtd_quant_method | |
50 #end if | |
51 #end if | |
52 #if $param_algorithm_epd_enabled: | |
53 -algorithm:epd:enabled | |
54 #if " " in str($param_algorithm_epd_enabled): | |
55 "$param_algorithm_epd_enabled" | |
56 #else | |
57 $param_algorithm_epd_enabled | |
58 #end if | |
59 #end if | |
60 #if $param_algorithm_epd_width_filtering: | |
61 -algorithm:epd:width_filtering | |
62 #if " " in str($param_algorithm_epd_width_filtering): | |
63 "$param_algorithm_epd_width_filtering" | |
64 #else | |
65 $param_algorithm_epd_width_filtering | |
66 #end if | |
67 #end if | |
68 #if $param_algorithm_ffm_charge_lower_bound: | |
69 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound | |
70 #end if | |
71 #if $param_algorithm_ffm_charge_upper_bound: | |
72 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound | |
73 #end if | |
74 #if $param_algorithm_ffm_enable_RT_filtering: | |
75 -algorithm:ffm:enable_RT_filtering | |
76 #if " " in str($param_algorithm_ffm_enable_RT_filtering): | |
77 "$param_algorithm_ffm_enable_RT_filtering" | |
78 #else | |
79 $param_algorithm_ffm_enable_RT_filtering | |
80 #end if | |
81 #end if | |
82 #if $param_algorithm_ffm_isotope_filtering_model: | |
83 -algorithm:ffm:isotope_filtering_model | |
84 #if " " in str($param_algorithm_ffm_isotope_filtering_model): | |
85 "$param_algorithm_ffm_isotope_filtering_model" | |
86 #else | |
87 $param_algorithm_ffm_isotope_filtering_model | |
88 #end if | |
89 #end if | |
90 #if $param_algorithm_ffm_mz_scoring_13C: | |
91 -algorithm:ffm:mz_scoring_13C true | |
92 #end if | |
93 #if $param_algorithm_ffm_report_convex_hulls: | |
94 -algorithm:ffm:report_convex_hulls | |
95 #end if | |
96 #if $adv_opts.adv_opts_selector=='advanced': | |
97 #if $adv_opts.param_force: | |
98 -force | |
99 #end if | |
100 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: | |
101 -algorithm:mtd:trace_termination_criterion | |
102 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): | |
103 "$adv_opts.param_algorithm_mtd_trace_termination_criterion" | |
104 #else | |
105 $adv_opts.param_algorithm_mtd_trace_termination_criterion | |
106 #end if | |
107 #end if | |
108 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: | |
109 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers | |
110 #end if | |
111 #if $adv_opts.param_algorithm_mtd_min_sample_rate: | |
112 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate | |
113 #end if | |
114 #if $adv_opts.param_algorithm_mtd_min_trace_length: | |
115 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length | |
116 #end if | |
117 #if $adv_opts.param_algorithm_mtd_max_trace_length: | |
118 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length | |
119 #end if | |
120 #if $adv_opts.param_algorithm_epd_min_fwhm: | |
121 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm | |
122 #end if | |
123 #if $adv_opts.param_algorithm_epd_max_fwhm: | |
124 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm | |
125 #end if | |
126 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering: | |
127 -algorithm:epd:masstrace_snr_filtering | |
128 #end if | |
129 #if $adv_opts.param_algorithm_ffm_local_rt_range: | |
130 -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range | |
131 #end if | |
132 #if $adv_opts.param_algorithm_ffm_local_mz_range: | |
133 -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range | |
134 #end if | |
135 #if $adv_opts.param_algorithm_ffm_report_summed_ints: | |
136 -algorithm:ffm:report_summed_ints | |
137 #end if | |
138 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities: | |
139 -algorithm:ffm:use_smoothed_intensities | |
140 #if " " in str($adv_opts.param_algorithm_ffm_use_smoothed_intensities): | |
141 "$adv_opts.param_algorithm_ffm_use_smoothed_intensities" | |
142 #else | |
143 $adv_opts.param_algorithm_ffm_use_smoothed_intensities | |
144 #end if | |
145 #end if | |
146 #end if | |
147 ]]></command> | |
148 <inputs> | 56 <inputs> |
149 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/> | 57 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Centroided mzML file" help=" select mzml data sets(s)"/> |
150 <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/> | 58 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
151 <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/> | 59 <section name="common" title="Common parameters for all other subsections" help="" expanded="false"> |
152 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/> | 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=""/> |
153 <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/> | 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=""/> |
154 <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) "> | 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=""/> |
155 <option value="true" selected="true">true</option> | 63 </section> |
156 <option value="false">false</option> | 64 <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false"> |
157 </param> | 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=""/> |
158 <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data"> | 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=""/> |
159 <option value="area" selected="true">area</option> | 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"> |
160 <option value="median">median</option> | 68 <option value="area" selected="true">area</option> |
161 </param> | 69 <option value="median">median</option> |
162 <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="(-enabled) Disable for direct injection"> | 70 <option value="max_height">max_height</option> |
163 <option value="true" selected="true">true</option> | 71 <expand macro="list_string_san"/> |
164 <option value="false">false</option> | 72 </param> |
165 </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"> |
166 <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) 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"> | 74 <option value="outlier" selected="true">outlier</option> |
167 <option value="off">off</option> | 75 <option value="sample_rate">sample_rate</option> |
168 <option value="fixed" selected="true">fixed</option> | 76 <expand macro="list_string_san"/> |
169 <option value="auto">auto</option> | 77 </param> |
170 </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=""/> |
171 <param name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help="(-charge_lower_bound) "/> | 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=""/> |
172 <param name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help="(-charge_upper_bound) "/> | 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=""/> |
173 <param name="param_algorithm_ffm_enable_RT_filtering" display="radio" type="select" optional="False" value="true" label="Require sufficient overlap in RT while assembling mass traces" help="(-enable_RT_filtering) Disable for direct injection data"> | 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"/> |
174 <option value="false">false</option> | 82 </section> |
175 <option value="true" selected="true">true</option> | 83 <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false"> |
176 </param> | 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"/> |
177 <param name="param_algorithm_ffm_isotope_filtering_model" display="radio" type="select" optional="False" value="metabolites (5% RMS)" label="Remove/score candidate assemblies based on isotope intensities" help="(-isotope_filtering_model) 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"> | 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"> |
178 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> | 86 <option value="off">off</option> |
179 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> | 87 <option value="fixed" selected="true">fixed</option> |
180 <option value="peptides">peptides</option> | 88 <option value="auto">auto</option> |
181 <option value="none">none</option> | 89 <expand macro="list_string_san"/> |
182 <sanitizer> | 90 </param> |
183 <valid initial="string.printable"> | 91 <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/> |
184 <remove value="'"/> | 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"/> |
185 <remove value="""/> | 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=""/> |
186 </valid> | 94 </section> |
187 </sanitizer> | 95 <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false"> |
188 </param> | 96 <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=""/> |
189 <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" 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="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/> | 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=""/> |
190 <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/> | 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=""/> |
191 <expand macro="advanced_options"> | 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=""/> |
192 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 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=""/> |
193 <param name="param_algorithm_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) 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"> | 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"/> |
194 <option value="outlier" selected="true">outlier</option> | 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"> |
195 <option value="sample_rate">sample_rate</option> | 103 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> |
196 </param> | 104 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> |
197 <param name="param_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="(-trace_termination_outliers) "/> | 105 <option value="peptides">peptides</option> |
198 <param name="param_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="(-min_sample_rate) "/> | 106 <option value="none">none</option> |
199 <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/> | 107 <expand macro="list_string_san"/> |
200 <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/> | 108 </param> |
201 <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/> | 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.)"/> |
202 <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/> | 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=""/> |
203 <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/> | 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=""/> |
204 <param name="param_algorithm_ffm_local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help="(-local_rt_range) "/> | 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=""/> |
205 <param name="param_algorithm_ffm_local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help="(-local_mz_range) "/> | 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'"/> |
206 <param name="param_algorithm_ffm_report_summed_ints" display="radio" type="boolean" truevalue="-algorithm:ffm:report_summed_ints" falsevalue="" checked="false" optional="True" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help="(-report_summed_ints) "/> | 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=""> |
207 <param name="param_algorithm_ffm_use_smoothed_intensities" display="radio" type="select" optional="False" value="true" label="Use LOWESS intensities instead of raw intensities" help="(-use_smoothed_intensities) "> | 115 <expand macro="list_string_san"/> |
208 <option value="false">false</option> | 116 </param> |
209 <option value="true" selected="true">true</option> | 117 </section> |
118 </section> | |
119 <expand macro="adv_opts_macro"> | |
120 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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=""> | |
122 <expand macro="list_string_san"/> | |
210 </param> | 123 </param> |
211 </expand> | 124 </expand> |
125 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
126 <option value="out_chrom_FLAG">out_chrom (Elements assumes to be present in the sample (this influences isotope detection))</option> | |
127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
128 </param> | |
212 </inputs> | 129 </inputs> |
213 <outputs> | 130 <outputs> |
214 <data name="param_out" format="featurexml"/> | 131 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> |
215 <data name="param_out_chrom" format="mzml"/> | 132 <data name="out_chrom" label="${tool.name} on ${on_string}: out_chrom" format="mzml"> |
133 <filter>OPTIONAL_OUTPUTS is not None and "out_chrom_FLAG" in OPTIONAL_OUTPUTS</filter> | |
134 </data> | |
135 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
136 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
137 </data> | |
216 </outputs> | 138 </outputs> |
217 <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. | 139 <tests> |
140 <expand macro="autotest_FeatureFinderMetabo"/> | |
141 <expand macro="manutest_FeatureFinderMetabo"/> | |
142 </tests> | |
143 <help><![CDATA[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. | |
218 | 144 |
219 | 145 |
220 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help> | 146 For more information, visit http://www.openms.de/documentation/TOPP_FeatureFinderMetabo.html]]></help> |
147 <expand macro="references"/> | |
221 </tool> | 148 </tool> |