Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer
comparison SvmTheoreticalSpectrumGeneratorTrainer.xml @ 9:94b81345543d draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 19:57:32 +0000 |
parents | e98ae1229a67 |
children | b1a8601e2ea0 |
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8:a604e5e1bb06 | 9:94b81345543d |
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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> |