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comparison PrecursorIonSelector.xml @ 13:1cae2aac2260 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:21:13 +0000
parents fa7a58de2977
children
comparison
equal deleted inserted replaced
12:598f53ccd9b8 13:1cae2aac2260
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>PrecursorIonSelector</description> 5 <description>PrecursorIonSelector</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PrecursorIonSelector</token> 7 <token name="@EXECUTABLE@">PrecursorIonSelector</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@
104 <configfiles> 102 <configfiles>
105 <inputs name="args_json" data_style="paths"/> 103 <inputs name="args_json" data_style="paths"/>
106 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile> 104 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
107 </configfiles> 105 </configfiles>
108 <inputs> 106 <inputs>
109 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/> 107 <param argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
110 <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/> 108 <param argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
111 <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/> 109 <param argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
112 <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/> 110 <param argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
113 <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/> 111 <param argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
114 <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/> 112 <param argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
115 <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/> 113 <param argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
116 <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/> 114 <param argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
117 <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/> 115 <param argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
118 <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/> 116 <param argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
119 <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 117 <param argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
120 <expand macro="list_string_val"/> 118 <expand macro="list_string_val" name="fixed_modifications"/>
121 <expand macro="list_string_san"/> 119 <expand macro="list_string_san" name="fixed_modifications"/>
122 </param> 120 </param>
123 <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false"> 121 <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
124 <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help=""> 122 <param name="type" argument="-algorithm:type" type="select" optional="true" label="Strategy for precursor ion selection" help="">
125 <option value="ILP_IPS">ILP_IPS</option> 123 <option value="ILP_IPS">ILP_IPS</option>
126 <option value="IPS" selected="true">IPS</option> 124 <option value="IPS" selected="true">IPS</option>
127 <option value="SPS">SPS</option> 125 <option value="SPS">SPS</option>
128 <option value="Upshift">Upshift</option> 126 <option value="Upshift">Upshift</option>
129 <option value="Downshift">Downshift</option> 127 <option value="Downshift">Downshift</option>
130 <option value="DEX">DEX</option> 128 <option value="DEX">DEX</option>
131 <expand macro="list_string_san"/> 129 <expand macro="list_string_san" name="type"/>
132 </param> 130 </param>
133 <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/> 131 <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
134 <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/> 132 <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
135 <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/> 133 <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
136 <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/> 134 <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>
159 <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/> 157 <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
160 </section> 158 </section>
161 </section> 159 </section>
162 <section name="Preprocessing" title="" help="" expanded="false"> 160 <section name="Preprocessing" title="" help="" expanded="false">
163 <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/> 161 <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
164 <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help=""> 162 <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" type="select" optional="true" label="Precursor mass tolerance unit" help="">
165 <option value="ppm" selected="true">ppm</option> 163 <option value="ppm" selected="true">ppm</option>
166 <option value="Da">Da</option> 164 <option value="Da">Da</option>
167 <expand macro="list_string_san"/> 165 <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/>
168 </param> 166 </param>
169 <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help=""> 167 <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
170 <expand macro="list_string_san"/> 168 <expand macro="list_string_san" name="preprocessed_db_path"/>
171 </param> 169 </param>
172 <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> 170 <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
173 <expand macro="list_string_san"/> 171 <expand macro="list_string_san" name="preprocessed_db_pred_rt_path"/>
174 </param> 172 </param>
175 <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> 173 <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
176 <expand macro="list_string_san"/> 174 <expand macro="list_string_san" name="preprocessed_db_pred_dt_path"/>
177 </param> 175 </param>
178 <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/> 176 <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallelly predicted" help=""/>
179 <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/> 177 <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
180 <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help=""> 178 <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
181 <expand macro="list_string_san"/> 179 <expand macro="list_string_san" name="taxonomy"/>
182 </param> 180 </param>
183 <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help=""> 181 <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if peptide sequences should be stored" help=""/>
184 <expand macro="list_string_san"/>
185 </param>
186 <section name="rt_settings" title="" help="" expanded="false"> 182 <section name="rt_settings" title="" help="" expanded="false">
187 <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/> 183 <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
188 <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/> 184 <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
189 <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/> 185 <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
190 <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/> 186 <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
191 <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/> 187 <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
192 </section> 188 </section>
193 </section> 189 </section>
194 </section> 190 </section>
195 <expand macro="adv_opts_macro"> 191 <expand macro="adv_opts_macro">
196 <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help=""> 192 <param argument="-solver" type="select" optional="true" label="LP solver type" help="">
197 <option value="GLPK" selected="true">GLPK</option> 193 <option value="GLPK" selected="true">GLPK</option>
198 <option value="COINOR">COINOR</option> 194 <option value="COINOR">COINOR</option>
199 <expand macro="list_string_san"/> 195 <expand macro="list_string_san" name="solver"/>
200 </param> 196 </param>
201 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 197 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
202 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 198 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
203 <expand macro="list_string_san"/> 199 <expand macro="list_string_san" name="test"/>
204 </param> 200 </param>
205 </expand> 201 </expand>
206 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 202 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
207 <option value="out_FLAG">out (modified feature map)</option> 203 <option value="out_FLAG">out (modified feature map)</option>
208 <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option> 204 <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>
225 </data> 221 </data>
226 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 222 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
227 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 223 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
228 </data> 224 </data>
229 </outputs> 225 </outputs>
230 <tests> 226 <tests><!-- TOPP_PrecursorIonSelector_1 -->
231 <expand macro="autotest_PrecursorIonSelector"/> 227 <test expect_num_outputs="2">
232 <expand macro="manutest_PrecursorIonSelector"/> 228 <section name="adv_opts">
229 <param name="solver" value="GLPK"/>
230 <param name="force" value="false"/>
231 <param name="test" value="true"/>
232 </section>
233 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
234 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
235 <param name="num_precursors" value="1"/>
236 <param name="load_preprocessing" value="false"/>
237 <param name="store_preprocessing" value="false"/>
238 <param name="simulation" value="true"/>
239 <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
240 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
241 <param name="fixed_modifications" value=""/>
242 <section name="algorithm">
243 <param name="type" value="IPS"/>
244 <param name="max_iteration" value="10"/>
245 <param name="rt_bin_capacity" value="10"/>
246 <param name="step_size" value="1"/>
247 <param name="peptide_min_prob" value="0.2"/>
248 <param name="sequential_spectrum_order" value="false"/>
249 <section name="MIPFormulation">
250 <section name="thresholds">
251 <param name="min_protein_probability" value="0.2"/>
252 <param name="min_protein_id_probability" value="0.95"/>
253 <param name="min_pt_weight" value="0.5"/>
254 <param name="min_mz" value="500.0"/>
255 <param name="max_mz" value="5000.0"/>
256 <param name="min_pred_pep_prob" value="0.5"/>
257 <param name="min_rt_weight" value="0.5"/>
258 <param name="use_peptide_rule" value="true"/>
259 <param name="min_peptide_ids" value="2"/>
260 <param name="min_peptide_probability" value="0.95"/>
261 </section>
262 <section name="combined_ilp">
263 <param name="k1" value="0.2"/>
264 <param name="k2" value="0.2"/>
265 <param name="k3" value="0.4"/>
266 <param name="scale_matching_probs" value="true"/>
267 </section>
268 <section name="feature_based">
269 <param name="no_intensity_normalization" value="false"/>
270 <param name="max_number_precursors_per_feature" value="1"/>
271 </section>
272 </section>
273 <section name="Preprocessing">
274 <param name="precursor_mass_tolerance" value="0.9"/>
275 <param name="precursor_mass_tolerance_unit" value="Da"/>
276 <param name="preprocessed_db_path" value=""/>
277 <param name="preprocessed_db_pred_rt_path" value=""/>
278 <param name="preprocessed_db_pred_dt_path" value=""/>
279 <param name="max_peptides_per_run" value="100000"/>
280 <param name="missed_cleavages" value="1"/>
281 <param name="taxonomy" value=""/>
282 <param name="store_peptide_sequences" value="false"/>
283 <section name="rt_settings">
284 <param name="min_rt" value="960.0"/>
285 <param name="max_rt" value="3840.0"/>
286 <param name="rt_step_size" value="30.0"/>
287 <param name="gauss_mean" value="-1.0"/>
288 <param name="gauss_sigma" value="3.0"/>
289 </section>
290 </section>
291 </section>
292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
293 <output name="ctd_out" ftype="xml">
294 <assert_contents>
295 <is_valid_xml/>
296 </assert_contents>
297 </output>
298 </test>
299 <!-- TOPP_PrecursorIonSelector_2 -->
300 <test expect_num_outputs="2">
301 <section name="adv_opts">
302 <param name="solver" value="GLPK"/>
303 <param name="force" value="false"/>
304 <param name="test" value="true"/>
305 </section>
306 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
307 <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
308 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
309 <param name="num_precursors" value="1"/>
310 <param name="load_preprocessing" value="false"/>
311 <param name="store_preprocessing" value="false"/>
312 <param name="simulation" value="false"/>
313 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
314 <param name="fixed_modifications" value=""/>
315 <section name="algorithm">
316 <param name="type" value="IPS"/>
317 <param name="max_iteration" value="10"/>
318 <param name="rt_bin_capacity" value="10"/>
319 <param name="step_size" value="1"/>
320 <param name="peptide_min_prob" value="0.2"/>
321 <param name="sequential_spectrum_order" value="false"/>
322 <section name="MIPFormulation">
323 <section name="thresholds">
324 <param name="min_protein_probability" value="0.2"/>
325 <param name="min_protein_id_probability" value="0.95"/>
326 <param name="min_pt_weight" value="0.5"/>
327 <param name="min_mz" value="500.0"/>
328 <param name="max_mz" value="5000.0"/>
329 <param name="min_pred_pep_prob" value="0.5"/>
330 <param name="min_rt_weight" value="0.5"/>
331 <param name="use_peptide_rule" value="true"/>
332 <param name="min_peptide_ids" value="2"/>
333 <param name="min_peptide_probability" value="0.95"/>
334 </section>
335 <section name="combined_ilp">
336 <param name="k1" value="0.2"/>
337 <param name="k2" value="0.2"/>
338 <param name="k3" value="0.4"/>
339 <param name="scale_matching_probs" value="true"/>
340 </section>
341 <section name="feature_based">
342 <param name="no_intensity_normalization" value="false"/>
343 <param name="max_number_precursors_per_feature" value="1"/>
344 </section>
345 </section>
346 <section name="Preprocessing">
347 <param name="precursor_mass_tolerance" value="0.9"/>
348 <param name="precursor_mass_tolerance_unit" value="Da"/>
349 <param name="preprocessed_db_path" value=""/>
350 <param name="preprocessed_db_pred_rt_path" value=""/>
351 <param name="preprocessed_db_pred_dt_path" value=""/>
352 <param name="max_peptides_per_run" value="100000"/>
353 <param name="missed_cleavages" value="1"/>
354 <param name="taxonomy" value=""/>
355 <param name="store_peptide_sequences" value="false"/>
356 <section name="rt_settings">
357 <param name="min_rt" value="960.0"/>
358 <param name="max_rt" value="3840.0"/>
359 <param name="rt_step_size" value="30.0"/>
360 <param name="gauss_mean" value="-1.0"/>
361 <param name="gauss_sigma" value="3.0"/>
362 </section>
363 </section>
364 </section>
365 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
366 <output name="ctd_out" ftype="xml">
367 <assert_contents>
368 <is_valid_xml/>
369 </assert_contents>
370 </output>
371 </test>
233 </tests> 372 </tests>
234 <help><![CDATA[PrecursorIonSelector 373 <help><![CDATA[PrecursorIonSelector
235 374
236 375
237 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PrecursorIonSelector.html]]></help> 376 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorIonSelector.html]]></help>
238 <expand macro="references"/> 377 <expand macro="references"/>
239 </tool> 378 </tool>