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comparison FeatureFinderCentroided.xml @ 15:1a709ba66f2f 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 18:57:17 +0000
parents b57f420a47b9
children
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14:a3fc834f23ba 15:1a709ba66f2f
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="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Detects two-dimensional features in LC-MS data.</description> 5 <description>Detects two-dimensional features in LC-MS data.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderCentroided</token> 7 <token name="@EXECUTABLE@">FeatureFinderCentroided</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@
60 <configfiles> 58 <configfiles>
61 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
63 </configfiles> 61 </configfiles>
64 <inputs> 62 <inputs>
65 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 63 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
66 <param name="seeds" argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/> 64 <param argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/>
67 <section name="algorithm" title="Algorithm section" help="" expanded="false"> 65 <section name="algorithm" title="Algorithm section" help="" expanded="false">
68 <section name="debug" title="" help="" expanded="false"> 66 <section name="debug" title="" help="" expanded="false">
69 <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" optional="true" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/> 67 <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" optional="true" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/>
70 </section> 68 </section>
71 <section name="intensity" title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)" help="" expanded="false"> 69 <section name="intensity" title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)" help="" expanded="false">
73 </section> 71 </section>
74 <section name="mass_trace" title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)" help="" expanded="false"> 72 <section name="mass_trace" title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1)" help="" expanded="false">
75 <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/> 73 <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
76 <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" optional="true" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/> 74 <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" optional="true" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/>
77 <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" optional="true" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/> 75 <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" optional="true" min="0" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="This parameter should be well below 'min_spectra'!"/>
78 <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to seperate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/> 76 <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" optional="true" min="0.0" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="This parameter is important to separate overlapping elution peaks.. It should be increased if feature elution profiles fluctuate a lot"/>
79 </section> 77 </section>
80 <section name="isotopic_pattern" title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)" help="" expanded="false"> 78 <section name="isotopic_pattern" title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1)" help="" expanded="false">
81 <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" optional="true" min="1" value="1" label="Lowest charge to search fo" help=""/> 79 <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" optional="true" min="1" value="1" label="Lowest charge to search fo" help=""/>
82 <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" optional="true" min="1" value="4" label="Highest charge to search fo" help=""/> 80 <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" optional="true" min="1" value="4" label="Highest charge to search fo" help=""/>
83 <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/> 81 <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" optional="true" min="0.0" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="It should be larger than the m/z resolution of the instrument.. This value must be smaller than that 1/charge_high!"/>
98 <param name="min_score" argument="-algorithm:feature:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/> 96 <param name="min_score" argument="-algorithm:feature:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="Feature score threshold for a feature to be reported" help="The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
99 <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/> 97 <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/>
100 <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/> 98 <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Trace score threshold" help="Traces below this threshold are removed after the model fitting.. This parameter is important for features that overlap in m/z dimension"/>
101 <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="true" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/> 99 <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" optional="true" min="0.0" max="1.0" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help=""/>
102 <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="true" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/> 100 <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" optional="true" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/>
103 <param name="rt_shape" argument="-algorithm:feature:rt_shape" display="radio" type="select" optional="false" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used"> 101 <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" optional="true" label="Choose model used for RT profile fitting" help="If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
104 <option value="symmetric" selected="true">symmetric</option> 102 <option value="symmetric" selected="true">symmetric</option>
105 <option value="asymmetric">asymmetric</option> 103 <option value="asymmetric">asymmetric</option>
106 <expand macro="list_string_san"/> 104 <expand macro="list_string_san" name="rt_shape"/>
107 </param> 105 </param>
108 <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="true" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/> 106 <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" optional="true" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/>
109 <param name="reported_mz" argument="-algorithm:feature:reported_mz" display="radio" type="select" optional="false" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model"> 107 <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" optional="true" label="The mass type that is reported for features" help="'maximum' returns the m/z value of the highest mass trace.. 'average' returns the intensity-weighted average m/z value of all contained peaks.. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
110 <option value="maximum">maximum</option> 108 <option value="maximum">maximum</option>
111 <option value="average">average</option> 109 <option value="average">average</option>
112 <option value="monoisotopic" selected="true">monoisotopic</option> 110 <option value="monoisotopic" selected="true">monoisotopic</option>
113 <expand macro="list_string_san"/> 111 <expand macro="list_string_san" name="reported_mz"/>
114 </param> 112 </param>
115 </section> 113 </section>
116 <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false"> 114 <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false">
117 <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/> 115 <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help=""/>
118 <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" optional="true" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/> 116 <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" optional="true" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/>
119 <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/> 117 <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="The cutoff is typically a bit lower in this case"/>
120 </section> 118 </section>
121 </section> 119 </section>
122 <expand macro="adv_opts_macro"> 120 <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=""/> 121 <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=""> 122 <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"/> 123 <expand macro="list_string_san" name="test"/>
126 </param> 124 </param>
127 </expand> 125 </expand>
128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
129 <option value="out_mzq_FLAG">out_mzq (Optional output file of MzQuantML)</option> 127 <option value="out_mzq_FLAG">out_mzq (Optional output file of MzQuantML)</option>
130 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 128 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
137 </data> 135 </data>
138 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
139 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
140 </data> 138 </data>
141 </outputs> 139 </outputs>
142 <tests> 140 <tests><!-- TOPP_FeatureFinderCentroided_1 -->
143 <expand macro="autotest_FeatureFinderCentroided"/> 141 <test expect_num_outputs="2">
144 <expand macro="manutest_FeatureFinderCentroided"/> 142 <section name="adv_opts">
143 <param name="force" value="false"/>
144 <param name="test" value="true"/>
145 <param name="pseudo_rt_shift" value="500.0"/>
146 </section>
147 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
148 <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
149 <section name="algorithm">
150 <section name="intensity">
151 <param name="bins" value="1"/>
152 </section>
153 <section name="mass_trace">
154 <param name="mz_tolerance" value="0.02"/>
155 <param name="min_spectra" value="14"/>
156 <param name="max_missing" value="1"/>
157 <param name="slope_bound" value="0.1"/>
158 </section>
159 <section name="isotopic_pattern">
160 <param name="charge_low" value="2"/>
161 <param name="charge_high" value="2"/>
162 <param name="mz_tolerance" value="0.02"/>
163 <param name="intensity_percentage" value="10.0"/>
164 <param name="intensity_percentage_optional" value="0.1"/>
165 <param name="optional_fit_improvement" value="2.0"/>
166 <param name="mass_window_width" value="100.0"/>
167 <param name="abundance_12C" value="98.93"/>
168 <param name="abundance_14N" value="99.632"/>
169 </section>
170 <section name="seed">
171 <param name="min_score" value="0.8"/>
172 </section>
173 <section name="fit">
174 <param name="max_iterations" value="500"/>
175 </section>
176 <section name="feature">
177 <param name="min_score" value="0.7"/>
178 <param name="min_isotope_fit" value="0.8"/>
179 <param name="min_trace_score" value="0.5"/>
180 <param name="min_rt_span" value="0.333"/>
181 <param name="max_rt_span" value="2.5"/>
182 <param name="rt_shape" value="symmetric"/>
183 <param name="max_intersection" value="0.35"/>
184 <param name="reported_mz" value="monoisotopic"/>
185 </section>
186 <section name="user-seed">
187 <param name="rt_tolerance" value="5.0"/>
188 <param name="mz_tolerance" value="1.1"/>
189 <param name="min_score" value="0.5"/>
190 </section>
191 </section>
192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
193 <output name="ctd_out" ftype="xml">
194 <assert_contents>
195 <is_valid_xml/>
196 </assert_contents>
197 </output>
198 </test>
145 </tests> 199 </tests>
146 <help><![CDATA[Detects two-dimensional features in LC-MS data. 200 <help><![CDATA[Detects two-dimensional features in LC-MS data.
147 201
148 202
149 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderCentroided.html]]></help> 203 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderCentroided.html]]></help>
150 <expand macro="references"/> 204 <expand macro="references"/>
151 </tool> 205 </tool>