Mercurial > repos > galaxyp > openms_rtmodel
comparison RTModel.xml @ 12:0fc4aa40badb draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:13:44 +0000 |
parents | 654e2bf18e82 |
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11:2d9d6a94e286 | 12:0fc4aa40badb |
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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: [Peptide property prediction]--> | 3 <!--Proposed Tool Section: [Peptide property prediction]--> |
4 <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Trains a model for the retention time prediction of peptides from a training set.</description> | 5 <description>Trains a model for the retention time prediction of peptides from a training set.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">RTModel</token> | 7 <token name="@EXECUTABLE@">RTModel</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
82 <configfiles> | 80 <configfiles> |
83 <inputs name="args_json" data_style="paths"/> | 81 <inputs name="args_json" data_style="paths"/> |
84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 82 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
85 </configfiles> | 83 </configfiles> |
86 <inputs> | 84 <inputs> |
87 <param name="in" argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.. select idxml,txt data sets(s)"/> | 85 <param argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.. select idxml,txt data sets(s)"/> |
88 <param name="in_positive" argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/> | 86 <param argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/> |
89 <param name="in_negative" argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/> | 87 <param argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/> |
90 <param name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). "> | 88 <param argument="-svm_type" type="select" optional="true" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). "> |
91 <option value="NU_SVR" selected="true">NU_SVR</option> | 89 <option value="NU_SVR" selected="true">NU_SVR</option> |
92 <option value="NU_SVC">NU_SVC</option> | 90 <option value="NU_SVC">NU_SVC</option> |
93 <option value="EPSILON_SVR">EPSILON_SVR</option> | 91 <option value="EPSILON_SVR">EPSILON_SVR</option> |
94 <option value="C_SVC">C_SVC</option> | 92 <option value="C_SVC">C_SVC</option> |
95 <expand macro="list_string_san"/> | 93 <expand macro="list_string_san" name="svm_type"/> |
96 </param> | 94 </param> |
97 <param name="nu" argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/> | 95 <param argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/> |
98 <param name="p" argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/> | 96 <param argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/> |
99 <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/> | 97 <param argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/> |
100 <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" label="the kernel type of the svm" help=""> | 98 <param argument="-kernel_type" type="select" optional="true" label="the kernel type of the svm" help=""> |
101 <option value="LINEAR">LINEAR</option> | 99 <option value="LINEAR">LINEAR</option> |
102 <option value="RBF">RBF</option> | 100 <option value="RBF">RBF</option> |
103 <option value="POLY">POLY</option> | 101 <option value="POLY">POLY</option> |
104 <option value="OLIGO" selected="true">OLIGO</option> | 102 <option value="OLIGO" selected="true">OLIGO</option> |
105 <expand macro="list_string_san"/> | 103 <expand macro="list_string_san" name="kernel_type"/> |
106 </param> | 104 </param> |
107 <param name="degree" argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/> | 105 <param argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/> |
108 <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/> | 106 <param argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/> |
109 <param name="max_std" argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/> | 107 <param argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/> |
110 <param name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/> | 108 <param argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/> |
111 <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/> | 109 <param argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/> |
112 <param name="total_gradient_time" argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/> | 110 <param argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/> |
113 <param name="first_dim_rt" argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/> | 111 <param argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/> |
114 <param name="additive_cv" argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied" help="with the step size to get the new value"/> | 112 <param argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied" help="with the step size to get the new value"/> |
115 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false"> | 113 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false"> |
116 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/> | 114 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/> |
117 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/> | 115 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/> |
118 <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/> | 116 <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/> |
119 <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/> | 117 <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/> |
131 <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/> | 129 <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/> |
132 <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/> | 130 <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/> |
133 <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/> | 131 <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/> |
134 </section> | 132 </section> |
135 <expand macro="adv_opts_macro"> | 133 <expand macro="adv_opts_macro"> |
136 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 134 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
137 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 135 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
138 <expand macro="list_string_san"/> | 136 <expand macro="list_string_san" name="test"/> |
139 </param> | 137 </param> |
140 </expand> | 138 </expand> |
141 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 139 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
142 <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option> | 140 <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option> |
143 <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option> | 141 <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option> |
154 </data> | 152 </data> |
155 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 153 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
156 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 154 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
157 </data> | 155 </data> |
158 </outputs> | 156 </outputs> |
159 <tests> | 157 <tests><!-- TOPP_RTModel_1 --> |
160 <expand macro="autotest_RTModel"/> | 158 <test expect_num_outputs="2"> |
161 <expand macro="manutest_RTModel"/> | 159 <section name="adv_opts"> |
160 <param name="force" value="false"/> | |
161 <param name="test" value="true"/> | |
162 </section> | |
163 <param name="in" value="RTModel_1_input.idXML"/> | |
164 <output name="out" file="RTModel_1_output.model" compare="sim_size" delta_frac="0.7" ftype="txt"/> | |
165 <param name="svm_type" value="NU_SVR"/> | |
166 <param name="nu" value="0.5"/> | |
167 <param name="p" value="0.1"/> | |
168 <param name="c" value="0.1"/> | |
169 <param name="kernel_type" value="POLY"/> | |
170 <param name="degree" value="1"/> | |
171 <param name="border_length" value="22"/> | |
172 <param name="max_std" value="10.0"/> | |
173 <param name="k_mer_length" value="1"/> | |
174 <param name="sigma" value="5.0"/> | |
175 <param name="total_gradient_time" value="3000.0"/> | |
176 <param name="first_dim_rt" value="false"/> | |
177 <param name="additive_cv" value="false"/> | |
178 <section name="cv"> | |
179 <param name="skip_cv" value="true"/> | |
180 <param name="number_of_runs" value="10"/> | |
181 <param name="number_of_partitions" value="10"/> | |
182 <param name="degree_start" value="1"/> | |
183 <param name="degree_step_size" value="2"/> | |
184 <param name="degree_stop" value="4"/> | |
185 <param name="p_start" value="1.0"/> | |
186 <param name="p_step_size" value="10.0"/> | |
187 <param name="p_stop" value="1000.0"/> | |
188 <param name="c_start" value="1.0"/> | |
189 <param name="c_step_size" value="10.0"/> | |
190 <param name="c_stop" value="1000.0"/> | |
191 <param name="nu_start" value="0.3"/> | |
192 <param name="nu_step_size" value="1.2"/> | |
193 <param name="nu_stop" value="0.7"/> | |
194 <param name="sigma_start" value="1.0"/> | |
195 <param name="sigma_step_size" value="1.3"/> | |
196 <param name="sigma_stop" value="15.0"/> | |
197 </section> | |
198 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
199 <output name="ctd_out" ftype="xml"> | |
200 <assert_contents> | |
201 <is_valid_xml/> | |
202 </assert_contents> | |
203 </output> | |
204 </test> | |
205 <!-- TOPP_RTModel_2 --> | |
206 <test expect_num_outputs="2"> | |
207 <section name="adv_opts"> | |
208 <param name="force" value="false"/> | |
209 <param name="test" value="true"/> | |
210 </section> | |
211 <param name="in_positive" value="RTModel_2_input_positive.idXML"/> | |
212 <param name="in_negative" value="RTModel_2_input_negative.idXML"/> | |
213 <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> | |
214 <param name="svm_type" value="NU_SVR"/> | |
215 <param name="nu" value="0.5"/> | |
216 <param name="p" value="0.1"/> | |
217 <param name="c" value="0.5"/> | |
218 <param name="kernel_type" value="OLIGO"/> | |
219 <param name="degree" value="1"/> | |
220 <param name="border_length" value="22"/> | |
221 <param name="max_std" value="10.0"/> | |
222 <param name="k_mer_length" value="1"/> | |
223 <param name="sigma" value="5.0"/> | |
224 <param name="total_gradient_time" value="1.0"/> | |
225 <param name="first_dim_rt" value="false"/> | |
226 <param name="additive_cv" value="false"/> | |
227 <section name="cv"> | |
228 <param name="skip_cv" value="true"/> | |
229 <param name="number_of_runs" value="10"/> | |
230 <param name="number_of_partitions" value="10"/> | |
231 <param name="degree_start" value="1"/> | |
232 <param name="degree_step_size" value="2"/> | |
233 <param name="degree_stop" value="4"/> | |
234 <param name="p_start" value="1.0"/> | |
235 <param name="p_step_size" value="10.0"/> | |
236 <param name="p_stop" value="1000.0"/> | |
237 <param name="c_start" value="1.0"/> | |
238 <param name="c_step_size" value="10.0"/> | |
239 <param name="c_stop" value="1000.0"/> | |
240 <param name="nu_start" value="0.3"/> | |
241 <param name="nu_step_size" value="1.2"/> | |
242 <param name="nu_stop" value="0.7"/> | |
243 <param name="sigma_start" value="1.0"/> | |
244 <param name="sigma_step_size" value="1.3"/> | |
245 <param name="sigma_stop" value="15.0"/> | |
246 </section> | |
247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
248 <output name="ctd_out" ftype="xml"> | |
249 <assert_contents> | |
250 <is_valid_xml/> | |
251 </assert_contents> | |
252 </output> | |
253 </test> | |
254 <!-- TOPP_RTModel_3 --> | |
255 <test expect_num_outputs="2"> | |
256 <section name="adv_opts"> | |
257 <param name="force" value="false"/> | |
258 <param name="test" value="true"/> | |
259 </section> | |
260 <param name="in" value="RTModel_3_input.idXML"/> | |
261 <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> | |
262 <param name="svm_type" value="NU_SVR"/> | |
263 <param name="nu" value="0.5"/> | |
264 <param name="p" value="0.1"/> | |
265 <param name="c" value="0.001953125"/> | |
266 <param name="kernel_type" value="OLIGO"/> | |
267 <param name="degree" value="1"/> | |
268 <param name="border_length" value="22"/> | |
269 <param name="max_std" value="10.0"/> | |
270 <param name="k_mer_length" value="1"/> | |
271 <param name="sigma" value="1.0"/> | |
272 <param name="total_gradient_time" value="1.0"/> | |
273 <param name="first_dim_rt" value="false"/> | |
274 <param name="additive_cv" value="false"/> | |
275 <section name="cv"> | |
276 <param name="skip_cv" value="false"/> | |
277 <param name="number_of_runs" value="1"/> | |
278 <param name="number_of_partitions" value="5"/> | |
279 <param name="degree_start" value="1"/> | |
280 <param name="degree_step_size" value="2"/> | |
281 <param name="degree_stop" value="4"/> | |
282 <param name="p_start" value="1.0"/> | |
283 <param name="p_step_size" value="10.0"/> | |
284 <param name="p_stop" value="1000.0"/> | |
285 <param name="c_start" value="0.001953125"/> | |
286 <param name="c_step_size" value="2.0"/> | |
287 <param name="c_stop" value="0.001953125"/> | |
288 <param name="nu_start" value="0.4"/> | |
289 <param name="nu_step_size" value="1.2"/> | |
290 <param name="nu_stop" value="0.4"/> | |
291 <param name="sigma_start" value="5.0"/> | |
292 <param name="sigma_step_size" value="1.221055"/> | |
293 <param name="sigma_stop" value="5.0"/> | |
294 </section> | |
295 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
296 <output name="ctd_out" ftype="xml"> | |
297 <assert_contents> | |
298 <is_valid_xml/> | |
299 </assert_contents> | |
300 </output> | |
301 </test> | |
302 <!-- TOPP_RTModel_4 --> | |
303 <test expect_num_outputs="2"> | |
304 <section name="adv_opts"> | |
305 <param name="force" value="false"/> | |
306 <param name="test" value="true"/> | |
307 </section> | |
308 <param name="in" value="RTModel_4_input.txt" ftype="txt"/> | |
309 <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> | |
310 <param name="svm_type" value="NU_SVR"/> | |
311 <param name="nu" value="0.5"/> | |
312 <param name="p" value="0.1"/> | |
313 <param name="c" value="0.001953125"/> | |
314 <param name="kernel_type" value="OLIGO"/> | |
315 <param name="degree" value="1"/> | |
316 <param name="border_length" value="22"/> | |
317 <param name="max_std" value="10.0"/> | |
318 <param name="k_mer_length" value="1"/> | |
319 <param name="sigma" value="1.0"/> | |
320 <param name="total_gradient_time" value="1.0"/> | |
321 <param name="first_dim_rt" value="false"/> | |
322 <param name="additive_cv" value="false"/> | |
323 <section name="cv"> | |
324 <param name="skip_cv" value="false"/> | |
325 <param name="number_of_runs" value="1"/> | |
326 <param name="number_of_partitions" value="5"/> | |
327 <param name="degree_start" value="1"/> | |
328 <param name="degree_step_size" value="2"/> | |
329 <param name="degree_stop" value="4"/> | |
330 <param name="p_start" value="1.0"/> | |
331 <param name="p_step_size" value="10.0"/> | |
332 <param name="p_stop" value="1000.0"/> | |
333 <param name="c_start" value="0.001953125"/> | |
334 <param name="c_step_size" value="2.0"/> | |
335 <param name="c_stop" value="0.001953125"/> | |
336 <param name="nu_start" value="0.4"/> | |
337 <param name="nu_step_size" value="1.2"/> | |
338 <param name="nu_stop" value="0.4"/> | |
339 <param name="sigma_start" value="5.0"/> | |
340 <param name="sigma_step_size" value="1.221055"/> | |
341 <param name="sigma_stop" value="5.0"/> | |
342 </section> | |
343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
344 <output name="ctd_out" ftype="xml"> | |
345 <assert_contents> | |
346 <is_valid_xml/> | |
347 </assert_contents> | |
348 </output> | |
349 </test> | |
162 </tests> | 350 </tests> |
163 <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set. | 351 <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set. |
164 | 352 |
165 | 353 |
166 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_RTModel.html]]></help> | 354 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_RTModel.html]]></help> |
167 <expand macro="references"/> | 355 <expand macro="references"/> |
168 </tool> | 356 </tool> |