Mercurial > repos > galaxyp > openms_featurefindermetabo

comparison FeatureFinderMetabo.xml @ 12:d065d7f24654 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:46:43 -0400
parents a2007f7b7b6f
children dcf7cb579e98
comparison
equal deleted inserted replaced
11:0305f27fa06b 12:d065d7f24654
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 CTD2Galaxy.--> 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="2.2.0"> 4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.3.0">
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 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FeatureFinderMetabo 13 <command detect_errors="aggressive"><![CDATA[FeatureFinderMetabo
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
19 -out $param_out 19 -out $param_out
20 #end if
21 #if $param_out_chrom:
22 -out_chrom $param_out_chrom
20 #end if 23 #end if
21 #if $param_algorithm_common_noise_threshold_int: 24 #if $param_algorithm_common_noise_threshold_int:
22 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int 25 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
23 #end if 26 #end if
24 #if $param_algorithm_common_chrom_peak_snr: 27 #if $param_algorithm_common_chrom_peak_snr:
83 #else 86 #else
84 $param_algorithm_ffm_isotope_filtering_model 87 $param_algorithm_ffm_isotope_filtering_model
85 #end if 88 #end if
86 #end if 89 #end if
87 #if $param_algorithm_ffm_mz_scoring_13C: 90 #if $param_algorithm_ffm_mz_scoring_13C:
88 -algorithm:ffm:mz_scoring_13C 91 -algorithm:ffm:mz_scoring_13C true
89 #end if 92 #end if
90 #if $param_algorithm_ffm_report_convex_hulls: 93 #if $param_algorithm_ffm_report_convex_hulls:
91 -algorithm:ffm:report_convex_hulls 94 -algorithm:ffm:report_convex_hulls
92 #end if 95 #end if
93 #if $adv_opts.adv_opts_selector=='advanced': 96 #if $adv_opts.adv_opts_selector=='advanced':
139 #else 142 #else
140 $adv_opts.param_algorithm_ffm_use_smoothed_intensities 143 $adv_opts.param_algorithm_ffm_use_smoothed_intensities
141 #end if 144 #end if
142 #end if 145 #end if
143 #end if 146 #end if
144 </command> 147 ]]></command>
145 <inputs> 148 <inputs>
146 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/> 149 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
147 <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) "/> 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) "/>
148 <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) "/> 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) "/>
149 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/> 152 <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>
174 <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"> 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">
175 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option> 178 <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
176 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> 179 <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
177 <option value="peptides">peptides</option> 180 <option value="peptides">peptides</option>
178 <option value="none">none</option> 181 <option value="none">none</option>
182 <sanitizer>
183 <valid initial="string.printable">
184 <remove value="'"/>
185 <remove value="&quot;"/>
186 </valid>
187 </sanitizer>
179 </param> 188 </param>
180 <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.)"/> 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.)"/>
181 <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) "/> 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) "/>
182 <expand macro="advanced_options"> 191 <expand macro="advanced_options">
183 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 192 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
201 </param> 210 </param>
202 </expand> 211 </expand>
203 </inputs> 212 </inputs>
204 <outputs> 213 <outputs>
205 <data name="param_out" format="featurexml"/> 214 <data name="param_out" format="featurexml"/>
215 <data name="param_out_chrom" format="mzml"/>
206 </outputs> 216 </outputs>
207 <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 217 <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
208 218
209 219
210 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help> 220 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help>
211 </tool> 221 </tool>