Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer

comparison SvmTheoreticalSpectrumGeneratorTrainer.xml @ 13:3c5de1c6c08a 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 19:21:45 +0000
parents b1a8601e2ea0
children
comparison
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12:d351b67b5317 13:3c5de1c6c08a
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="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description> 5 <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token> 7 <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in_spectra" argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/> 46 <param argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/>
49 <param name="in_identifications" argument="-in_identifications" type="data" format="idxml" optional="false" label="Input file with corresponding sequences in idXML" help=" select idxml data sets(s)"/> 47 <param argument="-in_identifications" type="data" format="idxml" optional="false" label="Input file with corresponding sequences in idXML" help=" select idxml data sets(s)"/>
50 <param name="precursor_charge" argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/> 48 <param argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/>
51 <param name="write_training_files" argument="-write_training_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No models are trained but input training files for libSVM command line tools are produced" help=""/> 49 <param argument="-write_training_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No models are trained but input training files for libSVM command line tools are produced" help=""/>
52 <section name="algorithm" title="" help="" expanded="false"> 50 <section name="algorithm" title="" help="" expanded="false">
53 <param name="number_intensity_levels" argument="-algorithm:number_intensity_levels" type="integer" optional="true" value="7" label="The number of intensity bins (for secondary type models)" help=""/> 51 <param name="number_intensity_levels" argument="-algorithm:number_intensity_levels" type="integer" optional="true" value="7" label="The number of intensity bins (for secondary type models)" help=""/>
54 <param name="number_regions" argument="-algorithm:number_regions" type="integer" optional="true" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help=""/> 52 <param name="number_regions" argument="-algorithm:number_regions" type="integer" optional="true" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help=""/>
55 <param name="parent_tolerance" argument="-algorithm:parent_tolerance" type="float" optional="true" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help=""/> 53 <param name="parent_tolerance" argument="-algorithm:parent_tolerance" type="float" optional="true" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help=""/>
56 <param name="peak_tolerance" argument="-algorithm:peak_tolerance" type="float" optional="true" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help=""/> 54 <param name="peak_tolerance" argument="-algorithm:peak_tolerance" type="float" optional="true" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help=""/>
116 <param name="nu_stop" argument="-algorithm:svm:svr:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.6" label="stopping point of nu" help=""/> 114 <param name="nu_stop" argument="-algorithm:svm:svr:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.6" label="stopping point of nu" help=""/>
117 </section> 115 </section>
118 </section> 116 </section>
119 </section> 117 </section>
120 <expand macro="adv_opts_macro"> 118 <expand macro="adv_opts_macro">
121 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 119 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
122 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 120 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
123 <expand macro="list_string_san"/> 121 <expand macro="list_string_san" name="test"/>
124 </param> 122 </param>
125 </expand> 123 </expand>
126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 124 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
128 </param> 126 </param>
131 <data name="model_output_file" label="${tool.name} on ${on_string}: model_output_file" format="txt"/> 129 <data name="model_output_file" label="${tool.name} on ${on_string}: model_output_file" format="txt"/>
132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 130 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 131 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
134 </data> 132 </data>
135 </outputs> 133 </outputs>
136 <tests> 134 <tests><!-- -TODO model_output_file creates multiple files-->
137 <expand macro="autotest_SvmTheoreticalSpectrumGeneratorTrainer"/> 135 </tests>
138 <expand macro="manutest_SvmTheoreticalSpectrumGeneratorTrainer"/>
139 </tests>
140 <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator 136 <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
141 137
142 138
143 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help> 139 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help>
144 <expand macro="references"/> 140 <expand macro="references"/>
145 </tool> 141 </tool>