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comparison FeatureFinderMetaboIdent.xml @ 4:ae20e8a6d309 draft default tip

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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 19:09:59 +0000
parents 7e29bf457263
children
comparison
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3:dfc01523da09 4:ae20e8a6d309
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Detects features in MS1 data based on metabolite identifications.</description> 5 <description>Detects features in MS1 data based on metabolite identifications.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token> 7 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</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@
86 <configfiles> 84 <configfiles>
87 <inputs name="args_json" data_style="paths"/> 85 <inputs name="args_json" data_style="paths"/>
88 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
89 </configfiles> 87 </configfiles>
90 <inputs> 88 <inputs>
91 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/> 89 <param argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
92 <param name="id" argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/> 90 <param argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
93 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false"> 91 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
94 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/> 92 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
95 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each assay" help=""/> 93 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
96 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a compound" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/> 94 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
97 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If zero, calculated based on 'detect:peak_width'"/> 95 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
98 </section> 96 </section>
99 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false"> 97 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
100 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="5.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/> 98 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
101 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/> 99 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
102 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/> 100 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
103 </section> 101 </section>
104 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false"> 102 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
105 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of elution model to fit to features" help=""> 103 <param name="type" argument="-model:type" type="select" optional="true" label="Type of elution model to fit to features" help="">
106 <option value="symmetric" selected="true">symmetric</option> 104 <option value="symmetric" selected="true">symmetric</option>
107 <option value="asymmetric">asymmetric</option> 105 <option value="asymmetric">asymmetric</option>
108 <option value="none">none</option> 106 <option value="none">none</option>
109 <expand macro="list_string_san"/> 107 <expand macro="list_string_san" name="type"/>
110 </param> 108 </param>
111 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/> 109 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
112 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/> 110 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
113 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/> 111 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
114 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/> 112 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
117 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/> 115 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
118 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 116 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
119 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/> 117 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
120 </section> 118 </section>
121 </section> 119 </section>
120 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
121 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
122 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
123 </section>
122 <expand macro="adv_opts_macro"> 124 <expand macro="adv_opts_macro">
123 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 125 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
124 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 126 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
125 <expand macro="list_string_san"/> 127 <expand macro="list_string_san" name="test"/>
126 </param> 128 </param>
127 </expand> 129 </expand>
128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
129 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option> 131 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
130 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option> 132 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
131 <option value="candidates_out_FLAG">candidates_out (Output file: Feature candidates (before filtering and model fitting))</option> 133 <option value="candidates_out_FLAG">candidates_out (Optional output file with feature candidates)</option>
132 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option> 134 <option value="trafo_out_FLAG">trafo_out (Output file: Retention times (expected vs)</option>
133 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 135 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
134 </param> 136 </param>
135 </inputs> 137 </inputs>
136 <outputs> 138 <outputs>
149 </data> 151 </data>
150 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 152 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
151 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 153 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
152 </data> 154 </data>
153 </outputs> 155 </outputs>
154 <tests> 156 <tests><!-- UTILS_FeatureFinderMetaboIdent_1 -->
155 <expand macro="autotest_FeatureFinderMetaboIdent"/> 157 <test expect_num_outputs="2">
156 <expand macro="manutest_FeatureFinderMetaboIdent"/> 158 <section name="adv_opts">
159 <param name="force" value="false"/>
160 <param name="test" value="true"/>
161 </section>
162 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
163 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
164 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
165 <section name="extract">
166 <param name="mz_window" value="5.0"/>
167 <param name="rt_window" value="20.0"/>
168 <param name="n_isotopes" value="2"/>
169 <param name="isotope_pmin" value="0.0"/>
170 </section>
171 <section name="detect">
172 <param name="peak_width" value="3.0"/>
173 <param name="min_peak_width" value="0.2"/>
174 <param name="signal_to_noise" value="0.8"/>
175 </section>
176 <section name="model">
177 <param name="type" value="symmetric"/>
178 <param name="add_zeros" value="0.2"/>
179 <param name="unweighted_fit" value="false"/>
180 <param name="no_imputation" value="false"/>
181 <param name="each_trace" value="false"/>
182 <section name="check">
183 <param name="min_area" value="1.0"/>
184 <param name="boundaries" value="0.5"/>
185 <param name="width" value="10.0"/>
186 <param name="asymmetry" value="10.0"/>
187 </section>
188 </section>
189 <section name="EMGScoring">
190 <param name="max_iteration" value="100"/>
191 <param name="init_mom" value="false"/>
192 </section>
193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
194 <output name="ctd_out" ftype="xml">
195 <assert_contents>
196 <is_valid_xml/>
197 </assert_contents>
198 </output>
199 </test>
157 </tests> 200 </tests>
158 <help><![CDATA[Detects features in MS1 data based on metabolite identifications. 201 <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
159 202
160 203
161 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help> 204 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FeatureFinderMetaboIdent.html]]></help>
162 <expand macro="references"/> 205 <expand macro="references"/>
163 </tool> 206 </tool>