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comparison FileFilter.xml @ 0:fa19593551c6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:53:56 -0500
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children 020fc2600133
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-1:000000000000 0:fa19593551c6
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileFilter" name="FileFilter" version="2.1.0">
5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FileFilter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FileFilter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_out_type:
22 -out_type
23 #if " " in str($param_out_type):
24 "$param_out_type"
25 #else
26 $param_out_type
27 #end if
28 #end if
29 #if $param_rt:
30 -rt "$param_rt"
31 #end if
32 #if $param_mz:
33 -mz "$param_mz"
34 #end if
35 #if $param_int:
36 -int "$param_int"
37 #end if
38 #if $param_sort:
39 -sort
40 #end if
41 #if $param_peak_options_sn:
42 -peak_options:sn $param_peak_options_sn
43 #end if
44
45 #if $rep_param_peak_options_rm_pc_charge:
46 -peak_options:rm_pc_charge
47 #for token in $rep_param_peak_options_rm_pc_charge:
48 #if " " in str(token):
49 "$token.param_peak_options_rm_pc_charge"
50 #else
51 $token.param_peak_options_rm_pc_charge
52 #end if
53 #end for
54 #end if
55 #if $param_peak_options_pc_mz_range:
56 -peak_options:pc_mz_range "$param_peak_options_pc_mz_range"
57 #end if
58
59 #if $rep_param_peak_options_pc_mz_list:
60 -peak_options:pc_mz_list
61 #for token in $rep_param_peak_options_pc_mz_list:
62 #if " " in str(token):
63 "$token.param_peak_options_pc_mz_list"
64 #else
65 $token.param_peak_options_pc_mz_list
66 #end if
67 #end for
68 #end if
69
70 #if $rep_param_peak_options_level:
71 -peak_options:level
72 #for token in $rep_param_peak_options_level:
73 #if " " in str(token):
74 "$token.param_peak_options_level"
75 #else
76 $token.param_peak_options_level
77 #end if
78 #end for
79 #end if
80 #if $param_peak_options_sort_peaks:
81 -peak_options:sort_peaks
82 #end if
83 #if $param_peak_options_no_chromatograms:
84 -peak_options:no_chromatograms
85 #end if
86 #if $param_peak_options_remove_chromatograms:
87 -peak_options:remove_chromatograms
88 #end if
89 #if $param_peak_options_mz_precision:
90 -peak_options:mz_precision $param_peak_options_mz_precision
91 #end if
92 #if $param_peak_options_int_precision:
93 -peak_options:int_precision $param_peak_options_int_precision
94 #end if
95 #if $param_peak_options_indexed_file:
96 -peak_options:indexed_file
97 #end if
98 #if $param_peak_options_numpress_masstime:
99 -peak_options:numpress:masstime $param_peak_options_numpress_masstime
100 #end if
101 #if $param_peak_options_numpress_masstime_error:
102 -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error
103 #end if
104 #if $param_peak_options_numpress_intensity:
105 -peak_options:numpress:intensity $param_peak_options_numpress_intensity
106 #end if
107 #if $param_peak_options_numpress_intensity_error:
108 -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error
109 #end if
110 #if $param_spectra_remove_zoom:
111 -spectra:remove_zoom
112 #end if
113 #if $param_spectra_remove_mode:
114 -spectra:remove_mode
115 #if " " in str($param_spectra_remove_mode):
116 "$param_spectra_remove_mode"
117 #else
118 $param_spectra_remove_mode
119 #end if
120 #end if
121 #if $param_spectra_remove_activation:
122 -spectra:remove_activation
123 #if " " in str($param_spectra_remove_activation):
124 "$param_spectra_remove_activation"
125 #else
126 $param_spectra_remove_activation
127 #end if
128 #end if
129 #if $param_spectra_remove_collision_energy:
130 -spectra:remove_collision_energy "$param_spectra_remove_collision_energy"
131 #end if
132 #if $param_spectra_remove_isolation_window_width:
133 -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width"
134 #end if
135 #if $param_spectra_select_zoom:
136 -spectra:select_zoom
137 #end if
138 #if $param_spectra_select_mode:
139 -spectra:select_mode
140 #if " " in str($param_spectra_select_mode):
141 "$param_spectra_select_mode"
142 #else
143 $param_spectra_select_mode
144 #end if
145 #end if
146 #if $param_spectra_select_activation:
147 -spectra:select_activation
148 #if " " in str($param_spectra_select_activation):
149 "$param_spectra_select_activation"
150 #else
151 $param_spectra_select_activation
152 #end if
153 #end if
154 #if $param_spectra_select_collision_energy:
155 -spectra:select_collision_energy "$param_spectra_select_collision_energy"
156 #end if
157 #if $param_spectra_select_isolation_window_width:
158 -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width"
159 #end if
160 #if $param_spectra_select_polarity:
161 -spectra:select_polarity
162 #if " " in str($param_spectra_select_polarity):
163 "$param_spectra_select_polarity"
164 #else
165 $param_spectra_select_polarity
166 #end if
167 #end if
168 #if $param_feature_q:
169 -feature:q "$param_feature_q"
170 #end if
171
172 #if $rep_param_consensus_map:
173 -consensus:map
174 #for token in $rep_param_consensus_map:
175 #if " " in str(token):
176 "$token.param_consensus_map"
177 #else
178 $token.param_consensus_map
179 #end if
180 #end for
181 #end if
182 #if $param_consensus_map_and:
183 -consensus:map_and
184 #end if
185 #if $param_consensus_blackorwhitelist_blacklist:
186 -consensus:blackorwhitelist:blacklist $param_consensus_blackorwhitelist_blacklist
187 #end if
188 #if $param_consensus_blackorwhitelist_file:
189 -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file
190 #end if
191
192 #if $rep_param_consensus_blackorwhitelist_maps:
193 -consensus:blackorwhitelist:maps
194 #for token in $rep_param_consensus_blackorwhitelist_maps:
195 #if " " in str(token):
196 "$token.param_consensus_blackorwhitelist_maps"
197 #else
198 $token.param_consensus_blackorwhitelist_maps
199 #end if
200 #end for
201 #end if
202 #if $param_consensus_blackorwhitelist_rt:
203 -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt
204 #end if
205 #if $param_consensus_blackorwhitelist_mz:
206 -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz
207 #end if
208 #if $param_consensus_blackorwhitelist_use_ppm_tolerance:
209 -consensus:blackorwhitelist:use_ppm_tolerance
210 #end if
211 #if $param_f_and_c_charge:
212 -f_and_c:charge "$param_f_and_c_charge"
213 #end if
214 #if $param_f_and_c_size:
215 -f_and_c:size "$param_f_and_c_size"
216 #end if
217
218 #if $rep_param_f_and_c_remove_meta:
219 -f_and_c:remove_meta
220 #for token in $rep_param_f_and_c_remove_meta:
221 #if " " in str(token):
222 "$token.param_f_and_c_remove_meta"
223 #else
224 $token.param_f_and_c_remove_meta
225 #end if
226 #end for
227 #end if
228 #if $param_id_keep_best_score_id:
229 -id:keep_best_score_id
230 #end if
231
232 #if $rep_param_id_sequences_whitelist:
233 -id:sequences_whitelist
234 #for token in $rep_param_id_sequences_whitelist:
235 #if " " in str(token):
236 "$token.param_id_sequences_whitelist"
237 #else
238 $token.param_id_sequences_whitelist
239 #end if
240 #end for
241 #end if
242
243 #if $rep_param_id_accessions_whitelist:
244 -id:accessions_whitelist
245 #for token in $rep_param_id_accessions_whitelist:
246 #if " " in str(token):
247 "$token.param_id_accessions_whitelist"
248 #else
249 $token.param_id_accessions_whitelist
250 #end if
251 #end for
252 #end if
253 #if $param_id_remove_annotated_features:
254 -id:remove_annotated_features
255 #end if
256 #if $param_id_remove_unannotated_features:
257 -id:remove_unannotated_features
258 #end if
259 #if $param_id_remove_unassigned_ids:
260 -id:remove_unassigned_ids
261 #end if
262 #if $param_id_blacklist:
263 -id:blacklist $param_id_blacklist
264 #end if
265 #if $param_id_rt:
266 -id:rt $param_id_rt
267 #end if
268 #if $param_id_mz:
269 -id:mz $param_id_mz
270 #end if
271 #if $param_id_blacklist_imperfect:
272 -id:blacklist_imperfect
273 #end if
274 #if $param_algorithm_SignalToNoise_win_len:
275 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
276 #end if
277 #if $param_algorithm_SignalToNoise_bin_count:
278 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
279 #end if
280 #if $param_algorithm_SignalToNoise_min_required_elements:
281 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
282 #end if
283 #if $param_algorithm_SignalToNoise_write_log_messages:
284 -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
285 #end if
286 #if $adv_opts.adv_opts_selector=='advanced':
287 #if $adv_opts.param_force:
288 -force
289 #end if
290 #if $adv_opts.param_id_remove_clashes:
291 -id:remove_clashes
292 #end if
293 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
294 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
295 #end if
296 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
297 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
298 #end if
299 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
300 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
301 #end if
302 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
303 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
304 #end if
305 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
306 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
307 #end if
308 #end if
309 </command>
310 <inputs>
311 <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/>
312 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) ">
313 <option value="mzML">mzML</option>
314 <option value="featureXML">featureXML</option>
315 <option value="consensusXML">consensusXML</option>
316 </param>
317 <param name="param_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) ">
318 <sanitizer>
319 <valid initial="string.printable">
320 <remove value="'"/>
321 <remove value="&quot;"/>
322 </valid>
323 </sanitizer>
324 </param>
325 <param name="param_mz" type="text" size="30" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="(-mz) ">
326 <sanitizer>
327 <valid initial="string.printable">
328 <remove value="'"/>
329 <remove value="&quot;"/>
330 </valid>
331 </sanitizer>
332 </param>
333 <param name="param_int" type="text" size="30" value=":" label="Intensity range to extract" help="(-int) ">
334 <sanitizer>
335 <valid initial="string.printable">
336 <remove value="'"/>
337 <remove value="&quot;"/>
338 </valid>
339 </sanitizer>
340 </param>
341 <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
342 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
343 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" max="1" title="param_peak_options_rm_pc_charge">
344 <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!">
345 <sanitizer>
346 <valid initial="string.printable">
347 <remove value="'"/>
348 <remove value="&quot;"/>
349 </valid>
350 </sanitizer>
351 </param>
352 </repeat>
353 <param name="param_peak_options_pc_mz_range" type="text" size="30" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="(-pc_mz_range) Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
354 <sanitizer>
355 <valid initial="string.printable">
356 <remove value="'"/>
357 <remove value="&quot;"/>
358 </valid>
359 </sanitizer>
360 </param>
361 <repeat name="rep_param_peak_options_pc_mz_list" min="0" max="1" title="param_peak_options_pc_mz_list">
362 <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept">
363 <sanitizer>
364 <valid initial="string.printable">
365 <remove value="'"/>
366 <remove value="&quot;"/>
367 </valid>
368 </sanitizer>
369 </param>
370 </repeat>
371 <repeat name="rep_param_peak_options_level" min="0" max="1" title="param_peak_options_level">
372 <param name="param_peak_options_level" type="text" size="30" value="1 2 3" label="MS levels to extract" help="(-level) ">
373 <sanitizer>
374 <valid initial="string.printable">
375 <remove value="'"/>
376 <remove value="&quot;"/>
377 </valid>
378 </sanitizer>
379 </param>
380 </repeat>
381 <param name="param_peak_options_sort_peaks" display="radio" type="boolean" truevalue="-peak_options:sort_peaks" falsevalue="" checked="false" optional="True" label="Sorts the peaks according to m/z" help="(-sort_peaks) "/>
382 <param name="param_peak_options_no_chromatograms" display="radio" type="boolean" truevalue="-peak_options:no_chromatograms" falsevalue="" checked="false" optional="True" label="No conversion to space-saving real chromatograms," help="(-no_chromatograms) e.g. from SRM scans"/>
383 <param name="param_peak_options_remove_chromatograms" display="radio" type="boolean" truevalue="-peak_options:remove_chromatograms" falsevalue="" checked="false" optional="True" label="Removes chromatograms stored in a file" help="(-remove_chromatograms) "/>
384 <param name="param_peak_options_mz_precision" display="radio" type="select" optional="False" value="64" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="(-mz_precision) ">
385 <option value="32">32</option>
386 <option value="64" selected="true">64</option>
387 </param>
388 <param name="param_peak_options_int_precision" display="radio" type="select" optional="False" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) ">
389 <option value="32" selected="true">32</option>
390 <option value="64">64</option>
391 </param>
392 <param name="param_peak_options_indexed_file" display="radio" type="boolean" truevalue="-peak_options:indexed_file" falsevalue="" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file) "/>
393 <param name="param_peak_options_numpress_masstime" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) ">
394 <option value="none" selected="true">none</option>
395 <option value="linear">linear</option>
396 <option value="pic">pic</option>
397 <option value="slof">slof</option>
398 </param>
399 <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" help="(-masstime_error) "/>
400 <param name="param_peak_options_numpress_intensity" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) ">
401 <option value="none" selected="true">none</option>
402 <option value="linear">linear</option>
403 <option value="pic">pic</option>
404 <option value="slof">slof</option>
405 </param>
406 <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic)" help="(-intensity_error) "/>
407 <param name="param_spectra_remove_zoom" display="radio" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/>
408 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) ">
409 <option value="Unknown">Unknown</option>
410 <option value="MassSpectrum">MassSpectrum</option>
411 <option value="MS1Spectrum">MS1Spectrum</option>
412 <option value="MSnSpectrum">MSnSpectrum</option>
413 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
414 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
415 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
416 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
417 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
418 <option value="Precursor">Precursor</option>
419 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
420 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
421 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
422 <option value="Emission">Emission</option>
423 <option value="Absorbtion">Absorbtion</option>
424 </param>
425 <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) ">
426 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
427 <option value="Post-source decay">Post-source decay</option>
428 <option value="Plasma desorption">Plasma desorption</option>
429 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
430 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
431 <option value="Electron capture dissociation">Electron capture dissociation</option>
432 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
433 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
434 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
435 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
436 <option value="Photodissociation">Photodissociation</option>
437 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
438 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
439 </param>
440 <param name="param_spectra_remove_collision_energy" type="text" size="30" value=":" label="Remove MSn scans with a collision energy in the given interval" help="(-remove_collision_energy) ">
441 <sanitizer>
442 <valid initial="string.printable">
443 <remove value="'"/>
444 <remove value="&quot;"/>
445 </valid>
446 </sanitizer>
447 </param>
448 <param name="param_spectra_remove_isolation_window_width" type="text" size="30" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="(-remove_isolation_window_width) ">
449 <sanitizer>
450 <valid initial="string.printable">
451 <remove value="'"/>
452 <remove value="&quot;"/>
453 </valid>
454 </sanitizer>
455 </param>
456 <param name="param_spectra_select_zoom" display="radio" type="boolean" truevalue="-spectra:select_zoom" falsevalue="" checked="false" optional="True" label="Select zoom (enhanced resolution) scans" help="(-select_zoom) "/>
457 <param name="param_spectra_select_mode" type="select" optional="True" label="Selects scans by scan mode" help="(-select_mode) ">
458 <option value="Unknown">Unknown</option>
459 <option value="MassSpectrum">MassSpectrum</option>
460 <option value="MS1Spectrum">MS1Spectrum</option>
461 <option value="MSnSpectrum">MSnSpectrum</option>
462 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
463 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
464 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
465 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
466 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
467 <option value="Precursor">Precursor</option>
468 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
469 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
470 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
471 <option value="Emission">Emission</option>
472 <option value="Absorbtion">Absorbtion</option>
473 </param>
474 <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) ">
475 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
476 <option value="Post-source decay">Post-source decay</option>
477 <option value="Plasma desorption">Plasma desorption</option>
478 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
479 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
480 <option value="Electron capture dissociation">Electron capture dissociation</option>
481 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
482 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
483 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
484 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
485 <option value="Photodissociation">Photodissociation</option>
486 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
487 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
488 </param>
489 <param name="param_spectra_select_collision_energy" type="text" size="30" value=":" label="Select MSn scans with a collision energy in the given interval" help="(-select_collision_energy) ">
490 <sanitizer>
491 <valid initial="string.printable">
492 <remove value="'"/>
493 <remove value="&quot;"/>
494 </valid>
495 </sanitizer>
496 </param>
497 <param name="param_spectra_select_isolation_window_width" type="text" size="30" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="(-select_isolation_window_width) ">
498 <sanitizer>
499 <valid initial="string.printable">
500 <remove value="'"/>
501 <remove value="&quot;"/>
502 </valid>
503 </sanitizer>
504 </param>
505 <param name="param_spectra_select_polarity" display="radio" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity) ">
506 <option value="unknown">unknown</option>
507 <option value="positive">positive</option>
508 <option value="negative">negative</option>
509 </param>
510 <param name="param_feature_q" type="text" size="30" value=":" label="Overall quality range to extract [0:1]" help="(-q) ">
511 <sanitizer>
512 <valid initial="string.printable">
513 <remove value="'"/>
514 <remove value="&quot;"/>
515 </valid>
516 </sanitizer>
517 </param>
518 <repeat name="rep_param_consensus_map" min="0" max="1" title="param_consensus_map">
519 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
520 <sanitizer>
521 <valid initial="string.printable">
522 <remove value="'"/>
523 <remove value="&quot;"/>
524 </valid>
525 </sanitizer>
526 </param>
527 </repeat>
528 <param name="param_consensus_map_and" display="radio" type="boolean" truevalue="-consensus:map_and" falsevalue="" checked="false" optional="True" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help="(-map_and) "/>
529 <param name="param_consensus_blackorwhitelist_blacklist" display="radio" type="select" optional="False" value="true" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept">
530 <option value="false">false</option>
531 <option value="true" selected="true">true</option>
532 </param>
533 <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/>
534 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" max="1" title="param_consensus_blackorwhitelist_maps">
535 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
536 <sanitizer>
537 <valid initial="string.printable">
538 <remove value="'"/>
539 <remove value="&quot;"/>
540 </valid>
541 </sanitizer>
542 </param>
543 </repeat>
544 <param name="param_consensus_blackorwhitelist_rt" type="float" min="0.0" optional="True" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help="(-rt) "/>
545 <param name="param_consensus_blackorwhitelist_mz" type="float" min="0.0" optional="True" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help="(-mz) "/>
546 <param name="param_consensus_blackorwhitelist_use_ppm_tolerance" display="radio" type="boolean" truevalue="-consensus:blackorwhitelist:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If ppm tolerance should be used" help="(-use_ppm_tolerance) Otherwise Da are used"/>
547 <param name="param_f_and_c_charge" type="text" size="30" value=":" label="Charge range to extract" help="(-charge) ">
548 <sanitizer>
549 <valid initial="string.printable">
550 <remove value="'"/>
551 <remove value="&quot;"/>
552 </valid>
553 </sanitizer>
554 </param>
555 <param name="param_f_and_c_size" type="text" size="30" value=":" label="Size range to extract" help="(-size) ">
556 <sanitizer>
557 <valid initial="string.printable">
558 <remove value="'"/>
559 <remove value="&quot;"/>
560 </valid>
561 </sanitizer>
562 </param>
563 <repeat name="rep_param_f_and_c_remove_meta" min="0" max="1" title="param_f_and_c_remove_meta">
564 <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!">
565 <sanitizer>
566 <valid initial="string.printable">
567 <remove value="'"/>
568 <remove value="&quot;"/>
569 </valid>
570 </sanitizer>
571 </param>
572 </repeat>
573 <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/>
574 <repeat name="rep_param_id_sequences_whitelist" min="0" max="1" title="param_id_sequences_whitelist">
575 <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)">
576 <sanitizer>
577 <valid initial="string.printable">
578 <remove value="'"/>
579 <remove value="&quot;"/>
580 </valid>
581 </sanitizer>
582 </param>
583 </repeat>
584 <repeat name="rep_param_id_accessions_whitelist" min="0" max="1" title="param_id_accessions_whitelist">
585 <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN">
586 <sanitizer>
587 <valid initial="string.printable">
588 <remove value="'"/>
589 <remove value="&quot;"/>
590 </valid>
591 </sanitizer>
592 </param>
593 </repeat>
594 <param name="param_id_remove_annotated_features" display="radio" type="boolean" truevalue="-id:remove_annotated_features" falsevalue="" checked="false" optional="True" label="Remove features with annotations" help="(-remove_annotated_features) "/>
595 <param name="param_id_remove_unannotated_features" display="radio" type="boolean" truevalue="-id:remove_unannotated_features" falsevalue="" checked="false" optional="True" label="Remove features without annotations" help="(-remove_unannotated_features) "/>
596 <param name="param_id_remove_unassigned_ids" display="radio" type="boolean" truevalue="-id:remove_unassigned_ids" falsevalue="" checked="false" optional="True" label="Remove unassigned peptide identifications" help="(-remove_unassigned_ids) "/>
597 <param name="param_id_blacklist" type="data" format="idxml" optional="True" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'id:rt' and 'id:mz' options" help="(-blacklist) &lt;br&gt;This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches"/>
598 <param name="param_id_rt" type="float" min="0.0" optional="True" value="0.1" label="Retention tolerance [s] for precursor to id position" help="(-rt) "/>
599 <param name="param_id_mz" type="float" min="0.0" optional="True" value="0.001" label="m/z tolerance [Th] for precursor to id position" help="(-mz) "/>
600 <param name="param_id_blacklist_imperfect" display="radio" type="boolean" truevalue="-id:blacklist_imperfect" falsevalue="" checked="false" optional="True" label="Allow for mismatching precursor positions (see 'id:blacklist')" help="(-blacklist_imperfect) "/>
601 <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
602 <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
603 <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/>
604 <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
605 <option value="true" selected="true">true</option>
606 <option value="false">false</option>
607 </param>
608 <expand macro="advanced_options">
609 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
610 <param name="param_id_remove_clashes" display="radio" type="boolean" truevalue="-id:remove_clashes" falsevalue="" checked="false" optional="True" label="Remove features with id clashes (different sequences mapped to one feature)" help="(-remove_clashes) "/>
611 <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
612 <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/>
613 <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/>
614 <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/>
615 <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/>
616 </expand>
617 </inputs>
618 <outputs>
619 <data name="param_out" metadata_source="param_in" format="input"/>
620 </outputs>
621 <help>Extracts or manipulates portions of data from peak, feature or consensus-feature files.
622
623
624 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html</help>
625 </tool>