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
date Thu, 01 Dec 2022 19:13:44 +0000
parents 654e2bf18e82
children
comparison
equal deleted inserted replaced
11:2d9d6a94e286 12:0fc4aa40badb
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>