comparison FeatureFinderCentroided.xml @ 16:d0c5325cb998 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:46:07 +0000
parents 1a709ba66f2f
children
comparison
equal deleted inserted replaced
15:1a709ba66f2f 16:d0c5325cb998
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Detects two-dimensional features in LC-MS data</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderCentroided</token> 6 <token name="@EXECUTABLE@">FeatureFinderCentroided</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $seeds: 19 #if $seeds:
21 mkdir seeds && 20 mkdir seeds &&
22 ln -s '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' && 21 cp '$seeds' 'seeds/${re.sub("[^\w\-_]", "_", $seeds.element_identifier)}.$gxy2omsext($seeds.ext)' &&
23 #end if 22 #end if
24 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 23 #if "out_mzq_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir out_mzq && 24 mkdir out_mzq &&
26 #end if 25 #end if
27 26
58 <configfiles> 57 <configfiles>
59 <inputs name="args_json" data_style="paths"/> 58 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 59 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles> 60 </configfiles>
62 <inputs> 61 <inputs>
63 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 62 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
64 <param argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/> 63 <param argument="-seeds" type="data" format="featurexml" optional="true" label="User specified seed list" help=" select featurexml data sets(s)"/>
65 <section name="algorithm" title="Algorithm section" help="" expanded="false"> 64 <section name="algorithm" title="Algorithm section" help="" expanded="false">
66 <section name="debug" title="" help="" expanded="false"> 65 <section name="debug" title="" help="" expanded="false">
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=""/> 66 <param name="pseudo_rt_shift" argument="-algorithm:debug:pseudo_rt_shift" type="float" min="1.0" value="500.0" label="Pseudo RT shift used when" help=""/>
68 </section> 67 </section>
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"> 68 <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">
70 <param name="bins" argument="-algorithm:intensity:bins" type="integer" optional="true" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/> 69 <param name="bins" argument="-algorithm:intensity:bins" type="integer" min="1" value="10" label="Number of bins per dimension (RT and m/z)" help="The higher this value, the more local the intensity significance score is.. This parameter should be decreased, if the algorithm is used on small regions of a map"/>
71 </section> 70 </section>
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"> 71 <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">
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!"/> 72 <param name="mz_tolerance" argument="-algorithm:mass_trace:mz_tolerance" type="float" 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!"/>
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=""/> 73 <param name="min_spectra" argument="-algorithm:mass_trace:min_spectra" type="integer" min="1" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help=""/>
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'!"/> 74 <param name="max_missing" argument="-algorithm:mass_trace:max_missing" type="integer" 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'!"/>
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"/> 75 <param name="slope_bound" argument="-algorithm:mass_trace:slope_bound" type="float" 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"/>
77 </section> 76 </section>
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"> 77 <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">
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=""/> 78 <param name="charge_low" argument="-algorithm:isotopic_pattern:charge_low" type="integer" min="1" value="1" label="Lowest 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=""/> 79 <param name="charge_high" argument="-algorithm:isotopic_pattern:charge_high" type="integer" min="1" value="4" label="Highest charge to search fo" help=""/>
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!"/> 80 <param name="mz_tolerance" argument="-algorithm:isotopic_pattern:mz_tolerance" type="float" 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!"/>
82 <param name="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" optional="true" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/> 81 <param name="intensity_percentage" argument="-algorithm:isotopic_pattern:intensity_percentage" type="float" min="0.0" max="100.0" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help=""/>
83 <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" optional="true" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/> 82 <param name="intensity_percentage_optional" argument="-algorithm:isotopic_pattern:intensity_percentage_optional" type="float" min="0.0" max="100.0" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help=""/>
84 <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" optional="true" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/> 83 <param name="optional_fit_improvement" argument="-algorithm:isotopic_pattern:optional_fit_improvement" type="float" min="0.0" max="100.0" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help=""/>
85 <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" optional="true" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/> 84 <param name="mass_window_width" argument="-algorithm:isotopic_pattern:mass_window_width" type="float" min="1.0" max="200.0" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help=""/>
86 <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" optional="true" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/> 85 <param name="abundance_12C" argument="-algorithm:isotopic_pattern:abundance_12C" type="float" min="0.0" max="100.0" value="98.93" label="Rel" help="abundance of the light carbon. Modify if labeled"/>
87 <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" optional="true" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/> 86 <param name="abundance_14N" argument="-algorithm:isotopic_pattern:abundance_14N" type="float" min="0.0" max="100.0" value="99.632" label="Rel" help="abundance of the light nitrogen. Modify if labeled"/>
88 </section> 87 </section>
89 <section name="seed" title="Settings that determine which peaks are considered a seed" help="" expanded="false"> 88 <section name="seed" title="Settings that determine which peaks are considered a seed" help="" expanded="false">
90 <param name="min_score" argument="-algorithm:seed:min_score" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/> 89 <param name="min_score" argument="-algorithm:seed:min_score" type="float" min="0.0" max="1.0" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.. If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
91 </section> 90 </section>
92 <section name="fit" title="Settings for the model fitting" help="" expanded="false"> 91 <section name="fit" title="Settings for the model fitting" help="" expanded="false">
93 <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" optional="true" min="1" value="500" label="Maximum number of iterations of the fit" help=""/> 92 <param name="max_iterations" argument="-algorithm:fit:max_iterations" type="integer" min="1" value="500" label="Maximum number of iterations of the fit" help=""/>
94 </section> 93 </section>
95 <section name="feature" title="Settings for the features (intensity, quality assessment, ...)" help="" expanded="false"> 94 <section name="feature" title="Settings for the features (intensity, quality assessment, ...)" help="" expanded="false">
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"/> 95 <param name="min_score" argument="-algorithm:feature:min_score" type="float" 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"/>
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=""/> 96 <param name="min_isotope_fit" argument="-algorithm:feature:min_isotope_fit" type="float" min="0.0" max="1.0" value="0.8" label="Minimum isotope fit of the feature before model fitting" help=""/>
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"/> 97 <param name="min_trace_score" argument="-algorithm:feature:min_trace_score" type="float" 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"/>
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=""/> 98 <param name="min_rt_span" argument="-algorithm:feature:min_rt_span" type="float" 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=""/>
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=""/> 99 <param name="max_rt_span" argument="-algorithm:feature:max_rt_span" type="float" min="0.5" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help=""/>
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"> 100 <param name="rt_shape" argument="-algorithm:feature:rt_shape" type="select" 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">
102 <option value="symmetric" selected="true">symmetric</option> 101 <option value="symmetric" selected="true">symmetric</option>
103 <option value="asymmetric">asymmetric</option> 102 <option value="asymmetric">asymmetric</option>
104 <expand macro="list_string_san" name="rt_shape"/> 103 <expand macro="list_string_san" name="rt_shape"/>
105 </param> 104 </param>
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=""/> 105 <param name="max_intersection" argument="-algorithm:feature:max_intersection" type="float" min="0.0" max="1.0" value="0.35" label="Maximum allowed intersection of features" help=""/>
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"> 106 <param name="reported_mz" argument="-algorithm:feature:reported_mz" type="select" 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">
108 <option value="maximum">maximum</option> 107 <option value="maximum">maximum</option>
109 <option value="average">average</option> 108 <option value="average">average</option>
110 <option value="monoisotopic" selected="true">monoisotopic</option> 109 <option value="monoisotopic" selected="true">monoisotopic</option>
111 <expand macro="list_string_san" name="reported_mz"/> 110 <expand macro="list_string_san" name="reported_mz"/>
112 </param> 111 </param>
113 </section> 112 </section>
114 <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false"> 113 <section name="user-seed" title="Settings for user-specified seeds" help="" expanded="false">
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=""/> 114 <param name="rt_tolerance" argument="-algorithm:user-seed:rt_tolerance" type="float" min="0.0" value="5.0" label="Allowed RT 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=""/> 115 <param name="mz_tolerance" argument="-algorithm:user-seed:mz_tolerance" type="float" min="0.0" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help=""/>
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"/> 116 <param name="min_score" argument="-algorithm:user-seed:min_score" type="float" 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"/>
118 </section> 117 </section>
119 </section> 118 </section>
120 <expand macro="adv_opts_macro"> 119 <expand macro="adv_opts_macro">
121 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 120 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
122 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 121 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
123 <expand macro="list_string_san" name="test"/> 122 <expand macro="list_string_san" name="test"/>
124 </param> 123 </param>
125 </expand> 124 </expand>
126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
127 <option value="out_mzq_FLAG">out_mzq (Optional output file of MzQuantML)</option> 126 <option value="out_mzq_FLAG">out_mzq (Optional output file of MzQuantML)</option>
135 </data> 134 </data>
136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 135 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 136 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
138 </data> 137 </data>
139 </outputs> 138 </outputs>
140 <tests><!-- TOPP_FeatureFinderCentroided_1 --> 139 <tests>
140 <!-- TOPP_FeatureFinderCentroided_1 -->
141 <test expect_num_outputs="2"> 141 <test expect_num_outputs="2">
142 <section name="adv_opts"> 142 <section name="adv_opts">
143 <param name="force" value="false"/> 143 <param name="force" value="false"/>
144 <param name="test" value="true"/> 144 <param name="test" value="true"/>
145 <param name="pseudo_rt_shift" value="500.0"/> 145 <param name="pseudo_rt_shift" value="500.0"/>
146 </section> 146 </section>
147 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> 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"/> 148 <output name="out" value="FeatureFinderCentroided_1_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
149 <section name="algorithm"> 149 <section name="algorithm">
150 <section name="intensity"> 150 <section name="intensity">
151 <param name="bins" value="1"/> 151 <param name="bins" value="1"/>
152 </section> 152 </section>
153 <section name="mass_trace"> 153 <section name="mass_trace">
193 <output name="ctd_out" ftype="xml"> 193 <output name="ctd_out" ftype="xml">
194 <assert_contents> 194 <assert_contents>
195 <is_valid_xml/> 195 <is_valid_xml/>
196 </assert_contents> 196 </assert_contents>
197 </output> 197 </output>
198 <assert_stdout>
199 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
200 </assert_stdout>
198 </test> 201 </test>
199 </tests> 202 </tests>
200 <help><![CDATA[Detects two-dimensional features in LC-MS data. 203 <help><![CDATA[Detects two-dimensional features in LC-MS data.
201 204
202 205
203 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderCentroided.html]]></help> 206 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderCentroided.html]]></help>
204 <expand macro="references"/> 207 <expand macro="references"/>
205 </tool> 208 </tool>