Mercurial > repos > galaxyp > openms_peakpickerwavelet

comparison PeakPickerWavelet.xml @ 13:2077efa205de draft

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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 19:16:26 +0000
parents 341af0b11af9
children bf0b36140329
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12:3e817bdb6d2e 13:2077efa205de
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> 7 <token name="@EXECUTABLE@">PeakPickerWavelet</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
46 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> 44 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
47 <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/> 45 <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
48 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> 46 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
49 <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/> 47 <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/>
102 <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> 100 <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
103 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> 101 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
104 </section> 102 </section>
105 </section> 103 </section>
106 <expand macro="adv_opts_macro"> 104 <expand macro="adv_opts_macro">
107 <param name="write_peak_meta_data" argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/> 105 <param argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/>
108 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 106 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
109 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 107 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
110 <expand macro="list_string_san"/> 108 <expand macro="list_string_san" name="test"/>
111 </param> 109 </param>
112 </expand> 110 </expand>
113 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
114 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
115 </param> 113 </param>
118 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 116 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
119 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
120 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
121 </data> 119 </data>
122 </outputs> 120 </outputs>
123 <tests> 121 <tests><!-- TOPP_PeakPickerWavelet_1 -->
124 <expand macro="autotest_PeakPickerWavelet"/> 122 <test expect_num_outputs="2">
125 <expand macro="manutest_PeakPickerWavelet"/> 123 <section name="adv_opts">
124 <param name="write_peak_meta_data" value="true"/>
125 <param name="force" value="false"/>
126 <param name="test" value="true"/>
127 </section>
128 <param name="in" value="PeakPickerWavelet_input.mzML"/>
129 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
130 <section name="algorithm">
131 <param name="signal_to_noise" value="3.0"/>
132 <param name="centroid_percentage" value="0.6"/>
133 <param name="peak_width" value="0.2"/>
134 <param name="estimate_peak_width" value="false"/>
135 <param name="fwhm_lower_bound_factor" value="0.5"/>
136 <param name="fwhm_upper_bound_factor" value="20.0"/>
137 <section name="optimization">
138 <param name="iterations" value="400"/>
139 <section name="penalties">
140 <param name="position" value="0.0"/>
141 <param name="left_width" value="1.0"/>
142 <param name="right_width" value="1.0"/>
143 <param name="height" value="1.0"/>
144 </section>
145 <section name="2d">
146 <param name="tolerance_mz" value="2.2"/>
147 <param name="max_peak_distance" value="1.2"/>
148 </section>
149 </section>
150 <section name="thresholds">
151 <param name="peak_bound" value="100.0"/>
152 <param name="peak_bound_ms2_level" value="10.0"/>
153 <param name="correlation" value="0.5"/>
154 <param name="noise_level" value="0.1"/>
155 <param name="search_radius" value="3"/>
156 </section>
157 <section name="wavelet_transform">
158 <param name="spacing" value="0.001"/>
159 </section>
160 <section name="deconvolution">
161 <param name="deconvolution" value="false"/>
162 <param name="asym_threshold" value="0.3"/>
163 <param name="left_width" value="2.0"/>
164 <param name="right_width" value="2.0"/>
165 <param name="scaling" value="0.12"/>
166 <section name="fitting">
167 <param name="fwhm_threshold" value="0.7"/>
168 <param name="eps_abs" value="9.999999747378752e-06"/>
169 <param name="eps_rel" value="9.999999747378752e-06"/>
170 <param name="max_iteration" value="10"/>
171 <section name="penalties">
172 <param name="position" value="0.0"/>
173 <param name="height" value="1.0"/>
174 <param name="left_width" value="0.0"/>
175 <param name="right_width" value="0.0"/>
176 </section>
177 </section>
178 </section>
179 <section name="SignalToNoiseEstimationParameter">
180 <param name="max_intensity" value="-1"/>
181 <param name="auto_max_stdev_factor" value="3.0"/>
182 <param name="auto_max_percentile" value="95"/>
183 <param name="auto_mode" value="0"/>
184 <param name="win_len" value="200.0"/>
185 <param name="bin_count" value="30"/>
186 <param name="stdev_mp" value="3.0"/>
187 <param name="min_required_elements" value="10"/>
188 <param name="noise_for_empty_window" value="1e+20"/>
189 </section>
190 </section>
191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
192 <output name="ctd_out" ftype="xml">
193 <assert_contents>
194 <is_valid_xml/>
195 </assert_contents>
196 </output>
197 </test>
198 <!-- TOPP_PeakPickerWavelet_2 -->
199 <test expect_num_outputs="2">
200 <section name="adv_opts">
201 <param name="write_peak_meta_data" value="true"/>
202 <param name="force" value="false"/>
203 <param name="test" value="true"/>
204 </section>
205 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
206 <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
207 <section name="algorithm">
208 <param name="signal_to_noise" value="2.0"/>
209 <param name="centroid_percentage" value="0.8"/>
210 <param name="peak_width" value="0.15"/>
211 <param name="estimate_peak_width" value="false"/>
212 <param name="fwhm_lower_bound_factor" value="1.0"/>
213 <param name="fwhm_upper_bound_factor" value="20.0"/>
214 <section name="optimization">
215 <param name="iterations" value="400"/>
216 <section name="penalties">
217 <param name="position" value="0.0"/>
218 <param name="left_width" value="1.0"/>
219 <param name="right_width" value="1.0"/>
220 <param name="height" value="1.0"/>
221 </section>
222 <section name="2d">
223 <param name="tolerance_mz" value="2.2"/>
224 <param name="max_peak_distance" value="1.2"/>
225 </section>
226 </section>
227 <section name="thresholds">
228 <param name="peak_bound" value="200.0"/>
229 <param name="peak_bound_ms2_level" value="50.0"/>
230 <param name="correlation" value="0.5"/>
231 <param name="noise_level" value="0.1"/>
232 <param name="search_radius" value="3"/>
233 </section>
234 <section name="wavelet_transform">
235 <param name="spacing" value="0.001"/>
236 </section>
237 <section name="deconvolution">
238 <param name="deconvolution" value="true"/>
239 <param name="asym_threshold" value="0.3"/>
240 <param name="left_width" value="2.0"/>
241 <param name="right_width" value="2.0"/>
242 <param name="scaling" value="0.1"/>
243 <section name="fitting">
244 <param name="fwhm_threshold" value="0.7"/>
245 <param name="eps_abs" value="1e-05"/>
246 <param name="eps_rel" value="1e-05"/>
247 <param name="max_iteration" value="100"/>
248 <section name="penalties">
249 <param name="position" value="1.0"/>
250 <param name="height" value="1.0"/>
251 <param name="left_width" value="0.0"/>
252 <param name="right_width" value="0.0"/>
253 </section>
254 </section>
255 </section>
256 <section name="SignalToNoiseEstimationParameter">
257 <param name="max_intensity" value="-1"/>
258 <param name="auto_max_stdev_factor" value="3.0"/>
259 <param name="auto_max_percentile" value="95"/>
260 <param name="auto_mode" value="0"/>
261 <param name="win_len" value="200.0"/>
262 <param name="bin_count" value="30"/>
263 <param name="stdev_mp" value="3.0"/>
264 <param name="min_required_elements" value="10"/>
265 <param name="noise_for_empty_window" value="1e+20"/>
266 </section>
267 </section>
268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
269 <output name="ctd_out" ftype="xml">
270 <assert_contents>
271 <is_valid_xml/>
272 </assert_contents>
273 </output>
274 </test>
275 <!-- TOPP_PeakPickerWavelet_4 -->
276 <test expect_num_outputs="2">
277 <section name="adv_opts">
278 <param name="write_peak_meta_data" value="true"/>
279 <param name="force" value="false"/>
280 <param name="test" value="true"/>
281 </section>
282 <param name="in" value="PeakPickerWavelet_input.mzML"/>
283 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
284 <section name="algorithm">
285 <param name="signal_to_noise" value="3.0"/>
286 <param name="centroid_percentage" value="0.6"/>
287 <param name="peak_width" value="0.2"/>
288 <param name="estimate_peak_width" value="false"/>
289 <param name="fwhm_lower_bound_factor" value="0.5"/>
290 <param name="fwhm_upper_bound_factor" value="20.0"/>
291 <section name="optimization">
292 <param name="iterations" value="400"/>
293 <section name="penalties">
294 <param name="position" value="0.0"/>
295 <param name="left_width" value="1.0"/>
296 <param name="right_width" value="1.0"/>
297 <param name="height" value="1.0"/>
298 </section>
299 <section name="2d">
300 <param name="tolerance_mz" value="2.2"/>
301 <param name="max_peak_distance" value="1.2"/>
302 </section>
303 </section>
304 <section name="thresholds">
305 <param name="peak_bound" value="100.0"/>
306 <param name="peak_bound_ms2_level" value="10.0"/>
307 <param name="correlation" value="0.5"/>
308 <param name="noise_level" value="0.1"/>
309 <param name="search_radius" value="3"/>
310 </section>
311 <section name="wavelet_transform">
312 <param name="spacing" value="0.001"/>
313 </section>
314 <section name="deconvolution">
315 <param name="deconvolution" value="false"/>
316 <param name="asym_threshold" value="0.3"/>
317 <param name="left_width" value="2.0"/>
318 <param name="right_width" value="2.0"/>
319 <param name="scaling" value="0.12"/>
320 <section name="fitting">
321 <param name="fwhm_threshold" value="0.7"/>
322 <param name="eps_abs" value="9.999999747378752e-06"/>
323 <param name="eps_rel" value="9.999999747378752e-06"/>
324 <param name="max_iteration" value="10"/>
325 <section name="penalties">
326 <param name="position" value="0.0"/>
327 <param name="height" value="1.0"/>
328 <param name="left_width" value="0.0"/>
329 <param name="right_width" value="0.0"/>
330 </section>
331 </section>
332 </section>
333 <section name="SignalToNoiseEstimationParameter">
334 <param name="max_intensity" value="-1"/>
335 <param name="auto_max_stdev_factor" value="3.0"/>
336 <param name="auto_max_percentile" value="95"/>
337 <param name="auto_mode" value="0"/>
338 <param name="win_len" value="200.0"/>
339 <param name="bin_count" value="30"/>
340 <param name="stdev_mp" value="3.0"/>
341 <param name="min_required_elements" value="10"/>
342 <param name="noise_for_empty_window" value="1e+20"/>
343 </section>
344 </section>
345 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
346 <output name="ctd_out" ftype="xml">
347 <assert_contents>
348 <is_valid_xml/>
349 </assert_contents>
350 </output>
351 </test>
352 <!-- TOPP_PeakPickerWavelet_5 -->
353 <test expect_num_outputs="2">
354 <section name="adv_opts">
355 <param name="write_peak_meta_data" value="false"/>
356 <param name="force" value="false"/>
357 <param name="test" value="true"/>
358 </section>
359 <param name="in" value="PeakPickerWavelet_input.mzML"/>
360 <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
361 <section name="algorithm">
362 <param name="signal_to_noise" value="3.0"/>
363 <param name="centroid_percentage" value="0.6"/>
364 <param name="peak_width" value="0.2"/>
365 <param name="estimate_peak_width" value="false"/>
366 <param name="fwhm_lower_bound_factor" value="0.5"/>
367 <param name="fwhm_upper_bound_factor" value="20.0"/>
368 <section name="optimization">
369 <param name="iterations" value="400"/>
370 <section name="penalties">
371 <param name="position" value="0.0"/>
372 <param name="left_width" value="1.0"/>
373 <param name="right_width" value="1.0"/>
374 <param name="height" value="1.0"/>
375 </section>
376 <section name="2d">
377 <param name="tolerance_mz" value="2.2"/>
378 <param name="max_peak_distance" value="1.2"/>
379 </section>
380 </section>
381 <section name="thresholds">
382 <param name="peak_bound" value="100.0"/>
383 <param name="peak_bound_ms2_level" value="10.0"/>
384 <param name="correlation" value="0.5"/>
385 <param name="noise_level" value="0.1"/>
386 <param name="search_radius" value="3"/>
387 </section>
388 <section name="wavelet_transform">
389 <param name="spacing" value="0.001"/>
390 </section>
391 <section name="deconvolution">
392 <param name="deconvolution" value="false"/>
393 <param name="asym_threshold" value="0.3"/>
394 <param name="left_width" value="2.0"/>
395 <param name="right_width" value="2.0"/>
396 <param name="scaling" value="0.12"/>
397 <section name="fitting">
398 <param name="fwhm_threshold" value="0.7"/>
399 <param name="eps_abs" value="9.999999747378752e-06"/>
400 <param name="eps_rel" value="9.999999747378752e-06"/>
401 <param name="max_iteration" value="10"/>
402 <section name="penalties">
403 <param name="position" value="0.0"/>
404 <param name="height" value="1.0"/>
405 <param name="left_width" value="0.0"/>
406 <param name="right_width" value="0.0"/>
407 </section>
408 </section>
409 </section>
410 <section name="SignalToNoiseEstimationParameter">
411 <param name="max_intensity" value="-1"/>
412 <param name="auto_max_stdev_factor" value="3.0"/>
413 <param name="auto_max_percentile" value="95"/>
414 <param name="auto_mode" value="0"/>
415 <param name="win_len" value="200.0"/>
416 <param name="bin_count" value="30"/>
417 <param name="stdev_mp" value="3.0"/>
418 <param name="min_required_elements" value="10"/>
419 <param name="noise_for_empty_window" value="1e+20"/>
420 </section>
421 </section>
422 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
423 <output name="ctd_out" ftype="xml">
424 <assert_contents>
425 <is_valid_xml/>
426 </assert_contents>
427 </output>
428 </test>
126 </tests> 429 </tests>
127 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. 430 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
128 431
129 432
130 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeakPickerWavelet.html]]></help> 433 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerWavelet.html]]></help>
131 <expand macro="references"/> 434 <expand macro="references"/>
132 </tool> 435 </tool>