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comparison SvmTheoreticalSpectrumGeneratorTrainer.xml @ 9:94b81345543d draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 19:57:32 +0000
parents e98ae1229a67
children b1a8601e2ea0
comparison
equal deleted inserted replaced
8:a604e5e1bb06 9:94b81345543d
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="2.3.0"> 4 <tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[SvmTheoreticalSpectrumGeneratorTrainer 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in_spectra: 18 ## Preprocessing
16 -in_spectra $param_in_spectra 19 mkdir in_spectra &&
17 #end if 20 ln -s '$in_spectra' 'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)' &&
18 #if $param_in_identifications: 21 mkdir in_identifications &&
19 -in_identifications $param_in_identifications 22 ln -s '$in_identifications' 'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)' &&
20 #end if 23 mkdir model_output_file &&
21 #if $param_model_output_file: 24
22 -model_output_file $param_model_output_file 25 ## Main program call
23 #end if 26
24 #if $param_precursor_charge: 27 set -o pipefail &&
25 -precursor_charge $param_precursor_charge 28 @EXECUTABLE@ -write_ctd ./ &&
26 #end if 29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
27 #if $param_write_training_files: 30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
28 -write_training_files 31 -in_spectra
29 #end if 32 'in_spectra/${re.sub("[^\w\-_]", "_", $in_spectra.element_identifier)}.$gxy2omsext($in_spectra.ext)'
30 #if $param_algorithm_number_intensity_levels: 33 -in_identifications
31 -algorithm:number_intensity_levels $param_algorithm_number_intensity_levels 34 'in_identifications/${re.sub("[^\w\-_]", "_", $in_identifications.element_identifier)}.$gxy2omsext($in_identifications.ext)'
32 #end if 35 -model_output_file
33 #if $param_algorithm_number_regions: 36 'model_output_file/output.${gxy2omsext("txt")}'
34 -algorithm:number_regions $param_algorithm_number_regions 37
35 #end if 38 ## Postprocessing
36 #if $param_algorithm_parent_tolerance: 39 && mv 'model_output_file/output.${gxy2omsext("txt")}' '$model_output_file'
37 -algorithm:parent_tolerance $param_algorithm_parent_tolerance 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 #end if 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 #if $param_algorithm_peak_tolerance: 42 #end if]]></command>
40 -algorithm:peak_tolerance $param_algorithm_peak_tolerance 43 <configfiles>
41 #end if 44 <inputs name="args_json" data_style="paths"/>
42 #if $param_algorithm_add_b_ions: 45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 -algorithm:add_b_ions 46 </configfiles>
44 #if " " in str($param_algorithm_add_b_ions):
45 "$param_algorithm_add_b_ions"
46 #else
47 $param_algorithm_add_b_ions
48 #end if
49 #end if
50 #if $param_algorithm_add_y_ions:
51 -algorithm:add_y_ions
52 #if " " in str($param_algorithm_add_y_ions):
53 "$param_algorithm_add_y_ions"
54 #else
55 $param_algorithm_add_y_ions
56 #end if
57 #end if
58 #if $param_algorithm_add_a_ions:
59 -algorithm:add_a_ions
60 #end if
61 #if $param_algorithm_add_c_ions:
62 -algorithm:add_c_ions
63 #end if
64 #if $param_algorithm_add_x_ions:
65 -algorithm:add_x_ions
66 #end if
67 #if $param_algorithm_add_z_ions:
68 -algorithm:add_z_ions
69 #end if
70 #if $param_algorithm_add_losses:
71 -algorithm:add_losses
72 #end if
73 #if $param_algorithm_add_b2_ions:
74 -algorithm:add_b2_ions
75 #end if
76 #if $param_algorithm_add_y2_ions:
77 -algorithm:add_y2_ions
78 #end if
79 #if $param_algorithm_svm_svc_type:
80 -algorithm:svm:svc_type $param_algorithm_svm_svc_type
81 #end if
82 #if $param_algorithm_svm_svr_type:
83 -algorithm:svm:svr_type $param_algorithm_svm_svr_type
84 #end if
85 #if $param_algorithm_svm_scaling:
86 -algorithm:svm:scaling
87 #if " " in str($param_algorithm_svm_scaling):
88 "$param_algorithm_svm_scaling"
89 #else
90 $param_algorithm_svm_scaling
91 #end if
92 #end if
93 #if $param_algorithm_svm_scaling_lower:
94 -algorithm:svm:scaling_lower $param_algorithm_svm_scaling_lower
95 #end if
96 #if $param_algorithm_svm_scaling_upper:
97 -algorithm:svm:scaling_upper $param_algorithm_svm_scaling_upper
98 #end if
99 #if $param_algorithm_svm_n_fold:
100 -algorithm:svm:n_fold $param_algorithm_svm_n_fold
101 #end if
102 #if $param_algorithm_svm_grid:
103 -algorithm:svm:grid
104 #end if
105 #if $param_algorithm_svm_additive_cv:
106 -algorithm:svm:additive_cv
107 #end if
108 #if $param_algorithm_svm_svc_kernel_type:
109 -algorithm:svm:svc:kernel_type $param_algorithm_svm_svc_kernel_type
110 #end if
111 #if $param_algorithm_svm_svc_degree:
112 -algorithm:svm:svc:degree $param_algorithm_svm_svc_degree
113 #end if
114 #if $param_algorithm_svm_svc_gamma:
115 -algorithm:svm:svc:gamma $param_algorithm_svm_svc_gamma
116 #end if
117 #if $param_algorithm_svm_svc_C:
118 -algorithm:svm:svc:C $param_algorithm_svm_svc_C
119 #end if
120 #if $param_algorithm_svm_svc_nu:
121 -algorithm:svm:svc:nu $param_algorithm_svm_svc_nu
122 #end if
123 #if $param_algorithm_svm_svc_balancing:
124 -algorithm:svm:svc:balancing
125 #if " " in str($param_algorithm_svm_svc_balancing):
126 "$param_algorithm_svm_svc_balancing"
127 #else
128 $param_algorithm_svm_svc_balancing
129 #end if
130 #end if
131 #if $param_algorithm_svm_svc_degree_start:
132 -algorithm:svm:svc:degree_start $param_algorithm_svm_svc_degree_start
133 #end if
134 #if $param_algorithm_svm_svc_degree_step_size:
135 -algorithm:svm:svc:degree_step_size $param_algorithm_svm_svc_degree_step_size
136 #end if
137 #if $param_algorithm_svm_svc_degree_stop:
138 -algorithm:svm:svc:degree_stop $param_algorithm_svm_svc_degree_stop
139 #end if
140 #if $param_algorithm_svm_svc_gamma_start:
141 -algorithm:svm:svc:gamma_start $param_algorithm_svm_svc_gamma_start
142 #end if
143 #if $param_algorithm_svm_svc_gamma_step_size:
144 -algorithm:svm:svc:gamma_step_size $param_algorithm_svm_svc_gamma_step_size
145 #end if
146 #if $param_algorithm_svm_svc_gamma_stop:
147 -algorithm:svm:svc:gamma_stop $param_algorithm_svm_svc_gamma_stop
148 #end if
149 #if $param_algorithm_svm_svc_c_start:
150 -algorithm:svm:svc:c_start $param_algorithm_svm_svc_c_start
151 #end if
152 #if $param_algorithm_svm_svc_c_step_size:
153 -algorithm:svm:svc:c_step_size $param_algorithm_svm_svc_c_step_size
154 #end if
155 #if $param_algorithm_svm_svc_c_stop:
156 -algorithm:svm:svc:c_stop $param_algorithm_svm_svc_c_stop
157 #end if
158 #if $param_algorithm_svm_svc_nu_start:
159 -algorithm:svm:svc:nu_start $param_algorithm_svm_svc_nu_start
160 #end if
161 #if $param_algorithm_svm_svc_nu_step_size:
162 -algorithm:svm:svc:nu_step_size $param_algorithm_svm_svc_nu_step_size
163 #end if
164 #if $param_algorithm_svm_svc_nu_stop:
165 -algorithm:svm:svc:nu_stop $param_algorithm_svm_svc_nu_stop
166 #end if
167 #if $param_algorithm_svm_svr_kernel_type:
168 -algorithm:svm:svr:kernel_type $param_algorithm_svm_svr_kernel_type
169 #end if
170 #if $param_algorithm_svm_svr_degree:
171 -algorithm:svm:svr:degree $param_algorithm_svm_svr_degree
172 #end if
173 #if $param_algorithm_svm_svr_gamma:
174 -algorithm:svm:svr:gamma $param_algorithm_svm_svr_gamma
175 #end if
176 #if $param_algorithm_svm_svr_C:
177 -algorithm:svm:svr:C $param_algorithm_svm_svr_C
178 #end if
179 #if $param_algorithm_svm_svr_p:
180 -algorithm:svm:svr:p $param_algorithm_svm_svr_p
181 #end if
182 #if $param_algorithm_svm_svr_nu:
183 -algorithm:svm:svr:nu $param_algorithm_svm_svr_nu
184 #end if
185 #if $param_algorithm_svm_svr_degree_start:
186 -algorithm:svm:svr:degree_start $param_algorithm_svm_svr_degree_start
187 #end if
188 #if $param_algorithm_svm_svr_degree_step_size:
189 -algorithm:svm:svr:degree_step_size $param_algorithm_svm_svr_degree_step_size
190 #end if
191 #if $param_algorithm_svm_svr_degree_stop:
192 -algorithm:svm:svr:degree_stop $param_algorithm_svm_svr_degree_stop
193 #end if
194 #if $param_algorithm_svm_svr_gamma_start:
195 -algorithm:svm:svr:gamma_start $param_algorithm_svm_svr_gamma_start
196 #end if
197 #if $param_algorithm_svm_svr_gamma_step_size:
198 -algorithm:svm:svr:gamma_step_size $param_algorithm_svm_svr_gamma_step_size
199 #end if
200 #if $param_algorithm_svm_svr_gamma_stop:
201 -algorithm:svm:svr:gamma_stop $param_algorithm_svm_svr_gamma_stop
202 #end if
203 #if $param_algorithm_svm_svr_p_start:
204 -algorithm:svm:svr:p_start $param_algorithm_svm_svr_p_start
205 #end if
206 #if $param_algorithm_svm_svr_p_step_size:
207 -algorithm:svm:svr:p_step_size $param_algorithm_svm_svr_p_step_size
208 #end if
209 #if $param_algorithm_svm_svr_p_stop:
210 -algorithm:svm:svr:p_stop $param_algorithm_svm_svr_p_stop
211 #end if
212 #if $param_algorithm_svm_svr_c_start:
213 -algorithm:svm:svr:c_start $param_algorithm_svm_svr_c_start
214 #end if
215 #if $param_algorithm_svm_svr_c_step_size:
216 -algorithm:svm:svr:c_step_size $param_algorithm_svm_svr_c_step_size
217 #end if
218 #if $param_algorithm_svm_svr_c_stop:
219 -algorithm:svm:svr:c_stop $param_algorithm_svm_svr_c_stop
220 #end if
221 #if $param_algorithm_svm_svr_nu_start:
222 -algorithm:svm:svr:nu_start $param_algorithm_svm_svr_nu_start
223 #end if
224 #if $param_algorithm_svm_svr_nu_step_size:
225 -algorithm:svm:svr:nu_step_size $param_algorithm_svm_svr_nu_step_size
226 #end if
227 #if $param_algorithm_svm_svr_nu_stop:
228 -algorithm:svm:svr:nu_stop $param_algorithm_svm_svr_nu_stop
229 #end if
230 #if $adv_opts.adv_opts_selector=='advanced':
231 #if $adv_opts.param_force:
232 -force
233 #end if
234 #end if
235 ]]></command>
236 <inputs> 47 <inputs>
237 <param name="param_in_spectra" type="data" format="mzml" optional="False" label="Input Training Spectra in mzML" help="(-in_spectra) "/> 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)"/>
238 <param name="param_in_identifications" type="data" format="idxml" optional="False" label="Input file with corresponding sequences in idXML" help="(-in_identifications) "/> 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)"/>
239 <param name="param_precursor_charge" type="integer" min="1" max="3" optional="True" value="2" label="Precursor charge state used for model training" help="(-precursor_charge) "/> 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=""/>
240 <param name="param_write_training_files" display="radio" type="boolean" truevalue="-write_training_files" falsevalue="" checked="false" optional="True" label="No models are trained but input training files for libSVM command line tools are produced" help="(-write_training_files) "/> 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=""/>
241 <param name="param_algorithm_number_intensity_levels" type="integer" value="7" label="The number of intensity bins (for secondary type models)" help="(-number_intensity_levels) "/> 52 <section name="algorithm" title="" help="" expanded="false">
242 <param name="param_algorithm_number_regions" type="integer" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help="(-number_regions) "/> 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=""/>
243 <param name="param_algorithm_parent_tolerance" type="float" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help="(-parent_tolerance) "/> 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=""/>
244 <param name="param_algorithm_peak_tolerance" type="float" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help="(-peak_tolerance) "/> 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=""/>
245 <param name="param_algorithm_add_b_ions" display="radio" type="select" optional="False" value="true" label="Train simulator for b-ions" help="(-add_b_ions) "> 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=""/>
246 <option value="true" selected="true">true</option> 57 <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=""/>
247 <option value="false">false</option> 58 <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=""/>
59 <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=""/>
60 <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=""/>
61 <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=""/>
62 <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=""/>
63 <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=""/>
64 <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=""/>
65 <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=""/>
66 <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">
67 <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=""/>
68 <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=""/>
69 <param name="scaling" argument="-algorithm:svm:scaling" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Apply scaling of feature values" help=""/>
70 <param name="scaling_lower" argument="-algorithm:svm:scaling_lower" type="float" optional="true" value="0.0" label="Lower bound for scaling" help=""/>
71 <param name="scaling_upper" argument="-algorithm:svm:scaling_upper" type="float" optional="true" value="1.0" label="Upper bound for scaling" help=""/>
72 <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=""/>
73 <param name="grid" argument="-algorithm:svm:grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grid search" help=""/>
74 <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=""/>
75 <section name="svc" title="Parameters for svm - classification of missing/abundant" help="" expanded="false">
76 <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=""/>
77 <param name="degree" argument="-algorithm:svm:svc:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/>
78 <param name="gamma" argument="-algorithm:svm:svc:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/>
79 <param name="C" argument="-algorithm:svm:svc:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/>
80 <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=""/>
81 <param name="balancing" argument="-algorithm:svm:svc:balancing" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use class balanced SVC training" help=""/>
82 <param name="degree_start" argument="-algorithm:svm:svc:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
83 <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=""/>
84 <param name="degree_stop" argument="-algorithm:svm:svc:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
85 <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=""/>
86 <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=""/>
87 <param name="gamma_stop" argument="-algorithm:svm:svc:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/>
88 <param name="c_start" argument="-algorithm:svm:svc:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/>
89 <param name="c_step_size" argument="-algorithm:svm:svc:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/>
90 <param name="c_stop" argument="-algorithm:svm:svc:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/>
91 <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=""/>
92 <param name="nu_step_size" argument="-algorithm:svm:svc:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" help=""/>
93 <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=""/>
94 </section>
95 <section name="svr" title="Parameters for svm - regression of peak intensities" help="" expanded="false">
96 <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=""/>
97 <param name="degree" argument="-algorithm:svm:svr:degree" type="integer" optional="true" min="1" value="3" label="For POLY" help=""/>
98 <param name="gamma" argument="-algorithm:svm:svr:gamma" type="float" optional="true" min="0.0" value="0.0" label="For POLY/RBF/SIGMOID" help=""/>
99 <param name="C" argument="-algorithm:svm:svr:C" type="float" optional="true" value="1.0" label="Cost of constraint violation" help=""/>
100 <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=""/>
101 <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=""/>
102 <param name="degree_start" argument="-algorithm:svm:svr:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
103 <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=""/>
104 <param name="degree_stop" argument="-algorithm:svm:svr:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
105 <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=""/>
106 <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=""/>
107 <param name="gamma_stop" argument="-algorithm:svm:svr:gamma_stop" type="float" optional="true" value="0.1" label="stopping point of gamma" help=""/>
108 <param name="p_start" argument="-algorithm:svm:svr:p_start" type="float" optional="true" value="1e-05" label="starting point of p" help=""/>
109 <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=""/>
110 <param name="p_stop" argument="-algorithm:svm:svr:p_stop" type="float" optional="true" value="0.1" label="stopping point of p" help=""/>
111 <param name="c_start" argument="-algorithm:svm:svr:c_start" type="float" optional="true" value="0.1" label="starting point of c" help=""/>
112 <param name="c_step_size" argument="-algorithm:svm:svr:c_step_size" type="integer" optional="true" value="100" label="step size of c" help=""/>
113 <param name="c_stop" argument="-algorithm:svm:svr:c_stop" type="integer" optional="true" value="1000" label="stopping point of c" help=""/>
114 <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=""/>
115 <param name="nu_step_size" argument="-algorithm:svm:svr:nu_step_size" type="integer" optional="true" value="2" label="step size of nu" 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=""/>
117 </section>
118 </section>
119 </section>
120 <expand macro="adv_opts_macro">
121 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
123 <expand macro="list_string_san"/>
124 </param>
125 </expand>
126 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
127 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
248 </param> 128 </param>
249 <param name="param_algorithm_add_y_ions" display="radio" type="select" optional="False" value="true" label="Train simulator for y-ions" help="(-add_y_ions) ">
250 <option value="true" selected="true">true</option>
251 <option value="false">false</option>
252 </param>
253 <param name="param_algorithm_add_a_ions" display="radio" type="boolean" truevalue="-algorithm:add_a_ions" falsevalue="" checked="false" optional="True" label="Train simulator for a-ions" help="(-add_a_ions) "/>
254 <param name="param_algorithm_add_c_ions" display="radio" type="boolean" truevalue="-algorithm:add_c_ions" falsevalue="" checked="false" optional="True" label="Train simulator for c-ions" help="(-add_c_ions) "/>
255 <param name="param_algorithm_add_x_ions" display="radio" type="boolean" truevalue="-algorithm:add_x_ions" falsevalue="" checked="false" optional="True" label="Train simulator for x-ions" help="(-add_x_ions) "/>
256 <param name="param_algorithm_add_z_ions" display="radio" type="boolean" truevalue="-algorithm:add_z_ions" falsevalue="" checked="false" optional="True" label="Train simulator for z-ions" help="(-add_z_ions) "/>
257 <param name="param_algorithm_add_losses" display="radio" type="boolean" truevalue="-algorithm:add_losses" falsevalue="" checked="false" optional="True" label="Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions" help="(-add_losses) "/>
258 <param name="param_algorithm_add_b2_ions" display="radio" type="boolean" truevalue="-algorithm:add_b2_ions" falsevalue="" checked="false" optional="True" label="Train simulator for doubly charged b-ions" help="(-add_b2_ions) "/>
259 <param name="param_algorithm_add_y2_ions" display="radio" type="boolean" truevalue="-algorithm:add_y2_ions" falsevalue="" checked="false" optional="True" label="Train simulator for double charged y-ions" help="(-add_y2_ions) "/>
260 <param name="param_algorithm_svm_svc_type" type="integer" min="0" max="1" optional="True" value="0" label="Type of the SVC: 0=C_SVC 1=NU_SVC" help="(-svc_type) "/>
261 <param name="param_algorithm_svm_svr_type" type="integer" min="0" max="1" optional="True" value="1" label="Type of the SVR: 0=EPSILON_SVR 1=NU_SVR" help="(-svr_type) "/>
262 <param name="param_algorithm_svm_scaling" display="radio" type="select" optional="False" value="true" label="Apply scaling of feature values" help="(-scaling) ">
263 <option value="true" selected="true">true</option>
264 <option value="false">false</option>
265 </param>
266 <param name="param_algorithm_svm_scaling_lower" type="float" value="0.0" label="Lower bound for scaling" help="(-scaling_lower) "/>
267 <param name="param_algorithm_svm_scaling_upper" type="float" value="1.0" label="Upper bound for scaling" help="(-scaling_upper) "/>
268 <param name="param_algorithm_svm_n_fold" type="integer" min="1" optional="True" value="5" label="n_fold cross validation is performed" help="(-n_fold) "/>
269 <param name="param_algorithm_svm_grid" display="radio" type="boolean" truevalue="-algorithm:svm:grid" falsevalue="" checked="false" optional="True" label="Perform grid search" help="(-grid) "/>
270 <param name="param_algorithm_svm_additive_cv" display="radio" type="boolean" truevalue="-algorithm:svm:additive_cv" falsevalue="" checked="false" optional="True" label="Additive step size (if false multiplicative)" help="(-additive_cv) "/>
271 <param name="param_algorithm_svm_svc_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type) "/>
272 <param name="param_algorithm_svm_svc_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree) "/>
273 <param name="param_algorithm_svm_svc_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma) "/>
274 <param name="param_algorithm_svm_svc_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C) "/>
275 <param name="param_algorithm_svm_svc_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu) "/>
276 <param name="param_algorithm_svm_svc_balancing" display="radio" type="select" optional="False" value="true" label="Use class balanced SVC training" help="(-balancing) ">
277 <option value="true" selected="true">true</option>
278 <option value="false">false</option>
279 </param>
280 <param name="param_algorithm_svm_svc_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
281 <param name="param_algorithm_svm_svc_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
282 <param name="param_algorithm_svm_svc_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
283 <param name="param_algorithm_svm_svc_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start) "/>
284 <param name="param_algorithm_svm_svc_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size) "/>
285 <param name="param_algorithm_svm_svc_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop) "/>
286 <param name="param_algorithm_svm_svc_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start) "/>
287 <param name="param_algorithm_svm_svc_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size) "/>
288 <param name="param_algorithm_svm_svc_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop) "/>
289 <param name="param_algorithm_svm_svc_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
290 <param name="param_algorithm_svm_svc_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size) "/>
291 <param name="param_algorithm_svm_svc_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop) "/>
292 <param name="param_algorithm_svm_svr_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type) "/>
293 <param name="param_algorithm_svm_svr_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree) "/>
294 <param name="param_algorithm_svm_svr_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma) "/>
295 <param name="param_algorithm_svm_svr_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C) "/>
296 <param name="param_algorithm_svm_svr_p" type="float" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help="(-p) "/>
297 <param name="param_algorithm_svm_svr_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu) "/>
298 <param name="param_algorithm_svm_svr_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
299 <param name="param_algorithm_svm_svr_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
300 <param name="param_algorithm_svm_svr_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
301 <param name="param_algorithm_svm_svr_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start) "/>
302 <param name="param_algorithm_svm_svr_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size) "/>
303 <param name="param_algorithm_svm_svr_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop) "/>
304 <param name="param_algorithm_svm_svr_p_start" type="float" value="1e-05" label="starting point of p" help="(-p_start) "/>
305 <param name="param_algorithm_svm_svr_p_step_size" type="integer" value="100" label="step size point of p" help="(-p_step_size) "/>
306 <param name="param_algorithm_svm_svr_p_stop" type="float" value="0.1" label="stopping point of p" help="(-p_stop) "/>
307 <param name="param_algorithm_svm_svr_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start) "/>
308 <param name="param_algorithm_svm_svr_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size) "/>
309 <param name="param_algorithm_svm_svr_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop) "/>
310 <param name="param_algorithm_svm_svr_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
311 <param name="param_algorithm_svm_svr_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size) "/>
312 <param name="param_algorithm_svm_svr_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop) "/>
313 <expand macro="advanced_options">
314 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
315 </expand>
316 </inputs> 129 </inputs>
317 <outputs> 130 <outputs>
318 <data name="param_model_output_file" format="data"/> 131 <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">
133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
134 </data>
319 </outputs> 135 </outputs>
320 <help>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator 136 <tests>
137 <expand macro="autotest_SvmTheoreticalSpectrumGeneratorTrainer"/>
138 <expand macro="manutest_SvmTheoreticalSpectrumGeneratorTrainer"/>
139 </tests>
140 <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
321 141
322 142
323 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html</help> 143 For more information, visit http://www.openms.de/documentation/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help>
144 <expand macro="references"/>
324 </tool> 145 </tool>