Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer
annotate SvmTheoreticalSpectrumGeneratorTrainer.xml @ 13:3c5de1c6c08a draft default tip
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 |
| rev | line source |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
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6d9c00e778ff
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Utilities]--> |
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3c5de1c6c08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
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9
94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="requirements"/> |
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a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 @EXT_FOO@ |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 #import re |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 ## Preprocessing |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 mkdir in_spectra && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 ln -s '$in_spectra' 'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)' && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir in_identifications && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 ln -s '$in_identifications' 'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)' && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 mkdir model_output_file && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 ## Main program call |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 set -o pipefail && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 @EXECUTABLE@ -write_ctd ./ && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 -in_spectra |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)' |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 -in_identifications |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)' |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 -model_output_file |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 'model_output_file/output.${gxy2omsext("txt")}' |
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0
a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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35 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 ## Postprocessing |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 && mv 'model_output_file/output.${gxy2omsext("txt")}' '$model_output_file' |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 #end if]]></command> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 <configfiles> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 <inputs name="args_json" data_style="paths"/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 </configfiles> |
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0
a92f7bc73817
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 <inputs> |
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46 <param argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/> |
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3c5de1c6c08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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)"/> |
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3c5de1c6c08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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48 <param argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/> |
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3c5de1c6c08a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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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=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 <section name="algorithm" title="" help="" expanded="false"> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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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=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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55 <param name="add_b_ions" argument="-algorithm:add_b_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Train simulator for b-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 <param name="add_y_ions" argument="-algorithm:add_y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Train simulator for y-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 <param name="add_a_ions" argument="-algorithm:add_a_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for a-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 <param name="add_c_ions" argument="-algorithm:add_c_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for c-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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59 <param name="add_x_ions" argument="-algorithm:add_x_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for x-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 <param name="add_z_ions" argument="-algorithm:add_z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for z-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 <param name="add_losses" argument="-algorithm:add_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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62 <param name="add_b2_ions" argument="-algorithm:add_b2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for doubly charged b-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 <param name="add_y2_ions" argument="-algorithm:add_y2_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Train simulator for double charged y-ions" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <section name="svm" title="Parameters controlling SVM trainig behaviou" help="All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation" expanded="false"> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65 <param name="svc_type" argument="-algorithm:svm:svc_type" type="integer" optional="true" min="0" max="1" value="0" label="Type of the SVC: 0=C_SVC 1=NU_SVC" help=""/> |
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94b81345543d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <param name="svr_type" argument="-algorithm:svm:svr_type" type="integer" optional="true" min="0" max="1" value="1" label="Type of the SVR: 0=EPSILON_SVR 1=NU_SVR" help=""/> |
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67 <param name="scaling" argument="-algorithm:svm:scaling" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Apply scaling of feature values" help=""/> |
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68 <param name="scaling_lower" argument="-algorithm:svm:scaling_lower" type="float" optional="true" value="0.0" label="Lower bound for scaling" help=""/> |
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69 <param name="scaling_upper" argument="-algorithm:svm:scaling_upper" type="float" optional="true" value="1.0" label="Upper bound for scaling" help=""/> |
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70 <param name="n_fold" argument="-algorithm:svm:n_fold" type="integer" optional="true" min="1" value="5" label="n_fold cross validation is performed" help=""/> |
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71 <param name="grid" argument="-algorithm:svm:grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grid search" help=""/> |
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72 <param name="additive_cv" argument="-algorithm:svm:additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additive step size (if false multiplicative)" help=""/> |
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73 <section name="svc" title="Parameters for svm - classification of missing/abundant" help="" expanded="false"> |
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74 <param name="kernel_type" argument="-algorithm:svm:svc:kernel_type" type="integer" optional="true" min="0" max="3" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help=""/> |
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75 <param name="degree" argument="-algorithm:svm:svc:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/> |
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76 <param name="gamma" argument="-algorithm:svm:svc:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/> |
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77 <param name="C" argument="-algorithm:svm:svc:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/> |
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78 <param name="nu" argument="-algorithm:svm:svc:nu" type="float" optional="true" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help=""/> |
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79 <param name="balancing" argument="-algorithm:svm:svc:balancing" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use class balanced SVC training" help=""/> |
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80 <param name="degree_start" argument="-algorithm:svm:svc:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/> |
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81 <param name="degree_step_size" argument="-algorithm:svm:svc:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/> |
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82 <param name="degree_stop" argument="-algorithm:svm:svc:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/> |
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83 <param name="gamma_start" argument="-algorithm:svm:svc:gamma_start" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="starting point of gamma" help=""/> |
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84 <param name="gamma_step_size" argument="-algorithm:svm:svc:gamma_step_size" type="integer" optional="true" value="100" label="step size point of gamma" help=""/> |
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85 <param name="gamma_stop" argument="-algorithm:svm:svc:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/> |
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86 <param name="c_start" argument="-algorithm:svm:svc:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/> |
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87 <param name="c_step_size" argument="-algorithm:svm:svc:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/> |
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88 <param name="c_stop" argument="-algorithm:svm:svc:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/> |
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89 <param name="nu_start" argument="-algorithm:svm:svc:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/> |
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90 <param name="nu_step_size" argument="-algorithm:svm:svc:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" help=""/> |
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91 <param name="nu_stop" argument="-algorithm:svm:svc:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.6" label="stopping point of nu" help=""/> |
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92 </section> |
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93 <section name="svr" title="Parameters for svm - regression of peak intensities" help="" expanded="false"> |
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94 <param name="kernel_type" argument="-algorithm:svm:svr:kernel_type" type="integer" optional="true" min="0" max="3" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help=""/> |
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95 <param name="degree" argument="-algorithm:svm:svr:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/> |
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96 <param name="gamma" argument="-algorithm:svm:svr:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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97 <param name="C" argument="-algorithm:svm:svr:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/> |
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98 <param name="p" argument="-algorithm:svm:svr:p" type="float" optional="true" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help=""/> |
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99 <param name="nu" argument="-algorithm:svm:svr:nu" type="float" optional="true" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help=""/> |
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100 <param name="degree_start" argument="-algorithm:svm:svr:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/> |
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101 <param name="degree_step_size" argument="-algorithm:svm:svr:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/> |
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102 <param name="degree_stop" argument="-algorithm:svm:svr:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/> |
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103 <param name="gamma_start" argument="-algorithm:svm:svr:gamma_start" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="starting point of gamma" help=""/> |
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104 <param name="gamma_step_size" argument="-algorithm:svm:svr:gamma_step_size" type="integer" optional="true" value="100" label="step size point of gamma" help=""/> |
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105 <param name="gamma_stop" argument="-algorithm:svm:svr:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/> |
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106 <param name="p_start" argument="-algorithm:svm:svr:p_start" type="float" optional="true" value="1e-05" label="starting point of p" help=""/> |
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107 <param name="p_step_size" argument="-algorithm:svm:svr:p_step_size" type="integer" optional="true" value="100" label="step size point of p" help=""/> |
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108 <param name="p_stop" argument="-algorithm:svm:svr:p_stop" type="float" optional="true" value="0.1" label="stopping point of p" help=""/> |
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109 <param name="c_start" argument="-algorithm:svm:svr:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/> |
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110 <param name="c_step_size" argument="-algorithm:svm:svr:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/> |
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111 <param name="c_stop" argument="-algorithm:svm:svr:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/> |
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112 <param name="nu_start" argument="-algorithm:svm:svr:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/> |
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113 <param name="nu_step_size" argument="-algorithm:svm:svr:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" help=""/> |
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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=""/> |
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115 </section> |
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116 </section> |
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117 </section> |
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118 <expand macro="adv_opts_macro"> |
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119 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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120 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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121 <expand macro="list_string_san" name="test"/> |
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9
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122 </param> |
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123 </expand> |
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11
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124 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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9
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125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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126 </param> |
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127 </inputs> |
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128 <outputs> |
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129 <data name="model_output_file" label="${tool.name} on ${on_string}: model_output_file" format="txt"/> |
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130 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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131 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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132 </data> |
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133 </outputs> |
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134 <tests><!-- -TODO model_output_file creates multiple files--> |
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135 </tests> |
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136 <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator |
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137 |
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138 |
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139 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help> |
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140 <expand macro="references"/> |
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141 </tool> |