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comparison FileFilter.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="FileFilter" name="FileFilter" version="2.0.0">
3 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
4 <macros>
5 <token name="@EXECUTABLE@">FileFilter</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>FileFilter
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_out:
16 -out $param_out
17 #end if
18 #if $param_out_type:
19 -out_type
20 #if " " in str($param_out_type):
21 "$param_out_type"
22 #else
23 $param_out_type
24 #end if
25 #end if
26 #if $param_rt:
27 -rt "$param_rt"
28 #end if
29 #if $param_mz:
30 -mz "$param_mz"
31 #end if
32 #if $param_pc_mz:
33 -pc_mz "$param_pc_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 -threads \${GALAXY_SLOTS:-24}
42 #if $param_peak_options_sn:
43 -peak_options:sn $param_peak_options_sn
44 #end if
45
46 #if $rep_param_peak_options_rm_pc_charge:
47 -peak_options:rm_pc_charge
48 #for token in $rep_param_peak_options_rm_pc_charge:
49 #if " " in str(token):
50 "$token.param_peak_options_rm_pc_charge"
51 #else
52 $token.param_peak_options_rm_pc_charge
53 #end if
54 #end for
55 #end if
56
57 #if $rep_param_peak_options_level:
58 -peak_options:level
59 #for token in $rep_param_peak_options_level:
60 #if " " in str(token):
61 "$token.param_peak_options_level"
62 #else
63 $token.param_peak_options_level
64 #end if
65 #end for
66 #end if
67 #if $param_peak_options_sort_peaks:
68 -peak_options:sort_peaks
69 #end if
70 #if $param_peak_options_no_chromatograms:
71 -peak_options:no_chromatograms
72 #end if
73 #if $param_peak_options_remove_chromatograms:
74 -peak_options:remove_chromatograms
75 #end if
76 #if $param_peak_options_mz_precision:
77 -peak_options:mz_precision
78 #if " " in str($param_peak_options_mz_precision):
79 "$param_peak_options_mz_precision"
80 #else
81 $param_peak_options_mz_precision
82 #end if
83 #end if
84 #if $param_peak_options_int_precision:
85 -peak_options:int_precision
86 #if " " in str($param_peak_options_int_precision):
87 "$param_peak_options_int_precision"
88 #else
89 $param_peak_options_int_precision
90 #end if
91 #end if
92 #if $param_peak_options_indexed_file:
93 -peak_options:indexed_file
94 #end if
95 #if $param_peak_options_numpress_masstime:
96 -peak_options:numpress:masstime
97 #if " " in str($param_peak_options_numpress_masstime):
98 "$param_peak_options_numpress_masstime"
99 #else
100 $param_peak_options_numpress_masstime
101 #end if
102 #end if
103 #if $param_peak_options_numpress_masstime_error:
104 -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error
105 #end if
106 #if $param_peak_options_numpress_intensity:
107 -peak_options:numpress:intensity
108 #if " " in str($param_peak_options_numpress_intensity):
109 "$param_peak_options_numpress_intensity"
110 #else
111 $param_peak_options_numpress_intensity
112 #end if
113 #end if
114 #if $param_peak_options_numpress_intensity_error:
115 -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error
116 #end if
117 #if $param_spectra_remove_zoom:
118 -spectra:remove_zoom
119 #end if
120 #if $param_spectra_remove_mode:
121 -spectra:remove_mode
122 #if " " in str($param_spectra_remove_mode):
123 "$param_spectra_remove_mode"
124 #else
125 $param_spectra_remove_mode
126 #end if
127 #end if
128 #if $param_spectra_remove_activation:
129 -spectra:remove_activation
130 #if " " in str($param_spectra_remove_activation):
131 "$param_spectra_remove_activation"
132 #else
133 $param_spectra_remove_activation
134 #end if
135 #end if
136 #if $param_spectra_remove_collision_energy:
137 -spectra:remove_collision_energy "$param_spectra_remove_collision_energy"
138 #end if
139 #if $param_spectra_remove_isolation_window_width:
140 -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width"
141 #end if
142 #if $param_spectra_select_zoom:
143 -spectra:select_zoom
144 #end if
145 #if $param_spectra_select_mode:
146 -spectra:select_mode
147 #if " " in str($param_spectra_select_mode):
148 "$param_spectra_select_mode"
149 #else
150 $param_spectra_select_mode
151 #end if
152 #end if
153 #if $param_spectra_select_activation:
154 -spectra:select_activation
155 #if " " in str($param_spectra_select_activation):
156 "$param_spectra_select_activation"
157 #else
158 $param_spectra_select_activation
159 #end if
160 #end if
161 #if $param_spectra_select_collision_energy:
162 -spectra:select_collision_energy "$param_spectra_select_collision_energy"
163 #end if
164 #if $param_spectra_select_isolation_window_width:
165 -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width"
166 #end if
167 #if $param_spectra_select_polarity:
168 -spectra:select_polarity
169 #if " " in str($param_spectra_select_polarity):
170 "$param_spectra_select_polarity"
171 #else
172 $param_spectra_select_polarity
173 #end if
174 #end if
175 #if $param_feature_q:
176 -feature:q "$param_feature_q"
177 #end if
178
179 #if $rep_param_consensus_map:
180 -consensus:map
181 #for token in $rep_param_consensus_map:
182 #if " " in str(token):
183 "$token.param_consensus_map"
184 #else
185 $token.param_consensus_map
186 #end if
187 #end for
188 #end if
189 #if $param_consensus_map_and:
190 -consensus:map_and
191 #end if
192 #if $param_consensus_blackorwhitelist_blacklist:
193 -consensus:blackorwhitelist:blacklist
194 #end if
195 #if $param_consensus_blackorwhitelist_file:
196 -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file
197 #end if
198
199 #if $rep_param_consensus_blackorwhitelist_maps:
200 -consensus:blackorwhitelist:maps
201 #for token in $rep_param_consensus_blackorwhitelist_maps:
202 #if " " in str(token):
203 "$token.param_consensus_blackorwhitelist_maps"
204 #else
205 $token.param_consensus_blackorwhitelist_maps
206 #end if
207 #end for
208 #end if
209 #if $param_consensus_blackorwhitelist_rt:
210 -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt
211 #end if
212 #if $param_consensus_blackorwhitelist_mz:
213 -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz
214 #end if
215 #if $param_consensus_blackorwhitelist_use_ppm_tolerance:
216 -consensus:blackorwhitelist:use_ppm_tolerance
217 #end if
218 #if $param_f_and_c_charge:
219 -f_and_c:charge "$param_f_and_c_charge"
220 #end if
221 #if $param_f_and_c_size:
222 -f_and_c:size "$param_f_and_c_size"
223 #end if
224
225 #if $rep_param_f_and_c_remove_meta:
226 -f_and_c:remove_meta
227 #for token in $rep_param_f_and_c_remove_meta:
228 #if " " in str(token):
229 "$token.param_f_and_c_remove_meta"
230 #else
231 $token.param_f_and_c_remove_meta
232 #end if
233 #end for
234 #end if
235 #if $param_id_keep_best_score_id:
236 -id:keep_best_score_id
237 #end if
238
239 #if $rep_param_id_sequences_whitelist:
240 -id:sequences_whitelist
241 #for token in $rep_param_id_sequences_whitelist:
242 #if " " in str(token):
243 "$token.param_id_sequences_whitelist"
244 #else
245 $token.param_id_sequences_whitelist
246 #end if
247 #end for
248 #end if
249
250 #if $rep_param_id_accessions_whitelist:
251 -id:accessions_whitelist
252 #for token in $rep_param_id_accessions_whitelist:
253 #if " " in str(token):
254 "$token.param_id_accessions_whitelist"
255 #else
256 $token.param_id_accessions_whitelist
257 #end if
258 #end for
259 #end if
260 #if $param_id_remove_annotated_features:
261 -id:remove_annotated_features
262 #end if
263 #if $param_id_remove_unannotated_features:
264 -id:remove_unannotated_features
265 #end if
266 #if $param_id_remove_unassigned_ids:
267 -id:remove_unassigned_ids
268 #end if
269 #if $param_id_blacklist:
270 -id:blacklist $param_id_blacklist
271 #end if
272 #if $param_id_rt:
273 -id:rt $param_id_rt
274 #end if
275 #if $param_id_mz:
276 -id:mz $param_id_mz
277 #end if
278 #if $param_id_blacklist_imperfect:
279 -id:blacklist_imperfect
280 #end if
281 #if $param_algorithm_SignalToNoise_win_len:
282 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
283 #end if
284 #if $param_algorithm_SignalToNoise_bin_count:
285 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
286 #end if
287 #if $param_algorithm_SignalToNoise_min_required_elements:
288 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
289 #end if
290 #if $adv_opts.adv_opts_selector=='advanced':
291 #if $adv_opts.param_force:
292 -force
293 #end if
294 #if $adv_opts.param_id_remove_clashes:
295 -id:remove_clashes
296 #end if
297 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
298 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
299 #end if
300 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
301 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
302 #end if
303 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
304 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
305 #end if
306 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
307 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
308 #end if
309 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
310 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
311 #end if
312 #end if
313 </command>
314 <inputs>
315 <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/>
316 <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) ">
317 <option value="mzML">mzML</option>
318 <option value="featureXML">featureXML</option>
319 <option value="consensusXML">consensusXML</option>
320 </param>
321 <param name="param_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) ">
322 <sanitizer>
323 <valid initial="string.printable">
324 <remove value="'"/>
325 <remove value="&quot;"/>
326 </valid>
327 </sanitizer>
328 </param>
329 <param name="param_mz" type="text" size="30" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="(-mz) ">
330 <sanitizer>
331 <valid initial="string.printable">
332 <remove value="'"/>
333 <remove value="&quot;"/>
334 </valid>
335 </sanitizer>
336 </param>
337 <param name="param_pc_mz" type="text" size="30" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="(-pc_mz) 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">
338 <sanitizer>
339 <valid initial="string.printable">
340 <remove value="'"/>
341 <remove value="&quot;"/>
342 </valid>
343 </sanitizer>
344 </param>
345 <param name="param_int" type="text" size="30" value=":" label="Intensity range to extract" help="(-int) ">
346 <sanitizer>
347 <valid initial="string.printable">
348 <remove value="'"/>
349 <remove value="&quot;"/>
350 </valid>
351 </sanitizer>
352 </param>
353 <param name="param_sort" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
354 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
355 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge">
356 <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!">
357 <sanitizer>
358 <valid initial="string.printable">
359 <remove value="'"/>
360 <remove value="&quot;"/>
361 </valid>
362 </sanitizer>
363 </param>
364 </repeat>
365 <repeat name="rep_param_peak_options_level" min="0" max="1" title="param_peak_options_level">
366 <param name="param_peak_options_level" type="text" size="30" value="1 2 3" label="MS levels to extract" help="(-level) ">
367 <sanitizer>
368 <valid initial="string.printable">
369 <remove value="'"/>
370 <remove value="&quot;"/>
371 </valid>
372 </sanitizer>
373 </param>
374 </repeat>
375 <param name="param_peak_options_sort_peaks" type="boolean" truevalue="-peak_options:sort_peaks" falsevalue="" checked="false" optional="True" label="Sorts the peaks according to m/z" help="(-sort_peaks) "/>
376 <param name="param_peak_options_no_chromatograms" 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"/>
377 <param name="param_peak_options_remove_chromatograms" type="boolean" truevalue="-peak_options:remove_chromatograms" falsevalue="" checked="false" optional="True" label="Removes chromatograms stored in a file" help="(-remove_chromatograms) "/>
378 <param name="param_peak_options_mz_precision" type="select" optional="True" value="64" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="(-mz_precision) ">
379 <option value="32">32</option>
380 <option value="64">64</option>
381 </param>
382 <param name="param_peak_options_int_precision" type="select" optional="True" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) ">
383 <option value="32">32</option>
384 <option value="64">64</option>
385 </param>
386 <param name="param_peak_options_indexed_file" 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) "/>
387 <param name="param_peak_options_numpress_masstime" type="select" optional="True" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) ">
388 <option value="none">none</option>
389 <option value="linear">linear</option>
390 <option value="pic">pic</option>
391 <option value="slof">slof</option>
392 </param>
393 <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) "/>
394 <param name="param_peak_options_numpress_intensity" type="select" optional="True" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) ">
395 <option value="none">none</option>
396 <option value="linear">linear</option>
397 <option value="pic">pic</option>
398 <option value="slof">slof</option>
399 </param>
400 <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) "/>
401 <param name="param_spectra_remove_zoom" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/>
402 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) ">
403 <option value="Unknown">Unknown</option>
404 <option value="MassSpectrum">MassSpectrum</option>
405 <option value="MS1Spectrum">MS1Spectrum</option>
406 <option value="MSnSpectrum">MSnSpectrum</option>
407 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
408 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
409 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
410 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
411 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
412 <option value="Precursor">Precursor</option>
413 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
414 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
415 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
416 <option value="Emission">Emission</option>
417 <option value="Absorbtion">Absorbtion</option>
418 </param>
419 <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) ">
420 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
421 <option value="Post-source decay">Post-source decay</option>
422 <option value="Plasma desorption">Plasma desorption</option>
423 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
424 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
425 <option value="Electron capture dissociation">Electron capture dissociation</option>
426 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
427 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
428 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
429 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
430 <option value="Photodissociation">Photodissociation</option>
431 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
432 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
433 </param>
434 <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) ">
435 <sanitizer>
436 <valid initial="string.printable">
437 <remove value="'"/>
438 <remove value="&quot;"/>
439 </valid>
440 </sanitizer>
441 </param>
442 <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) ">
443 <sanitizer>
444 <valid initial="string.printable">
445 <remove value="'"/>
446 <remove value="&quot;"/>
447 </valid>
448 </sanitizer>
449 </param>
450 <param name="param_spectra_select_zoom" type="boolean" truevalue="-spectra:select_zoom" falsevalue="" checked="false" optional="True" label="Select zoom (enhanced resolution) scans" help="(-select_zoom) "/>
451 <param name="param_spectra_select_mode" type="select" optional="True" label="Selects scans by scan mode" help="(-select_mode) ">
452 <option value="Unknown">Unknown</option>
453 <option value="MassSpectrum">MassSpectrum</option>
454 <option value="MS1Spectrum">MS1Spectrum</option>
455 <option value="MSnSpectrum">MSnSpectrum</option>
456 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
457 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
458 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
459 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
460 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
461 <option value="Precursor">Precursor</option>
462 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
463 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
464 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
465 <option value="Emission">Emission</option>
466 <option value="Absorbtion">Absorbtion</option>
467 </param>
468 <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) ">
469 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
470 <option value="Post-source decay">Post-source decay</option>
471 <option value="Plasma desorption">Plasma desorption</option>
472 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
473 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
474 <option value="Electron capture dissociation">Electron capture dissociation</option>
475 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
476 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
477 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
478 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
479 <option value="Photodissociation">Photodissociation</option>
480 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
481 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
482 </param>
483 <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) ">
484 <sanitizer>
485 <valid initial="string.printable">
486 <remove value="'"/>
487 <remove value="&quot;"/>
488 </valid>
489 </sanitizer>
490 </param>
491 <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) ">
492 <sanitizer>
493 <valid initial="string.printable">
494 <remove value="'"/>
495 <remove value="&quot;"/>
496 </valid>
497 </sanitizer>
498 </param>
499 <param name="param_spectra_select_polarity" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity) ">
500 <option value="unknown">unknown</option>
501 <option value="positive">positive</option>
502 <option value="negative">negative</option>
503 </param>
504 <param name="param_feature_q" type="text" size="30" value=":" label="Overall quality range to extract [0:1]" help="(-q) ">
505 <sanitizer>
506 <valid initial="string.printable">
507 <remove value="'"/>
508 <remove value="&quot;"/>
509 </valid>
510 </sanitizer>
511 </param>
512 <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map">
513 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
514 <sanitizer>
515 <valid initial="string.printable">
516 <remove value="'"/>
517 <remove value="&quot;"/>
518 </valid>
519 </sanitizer>
520 </param>
521 </repeat>
522 <param name="param_consensus_map_and" 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) "/>
523 <param name="param_consensus_blackorwhitelist_blacklist" type="boolean" truevalue="-consensus:blackorwhitelist:blacklist" falsevalue="" checked="true" optional="True" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept"/>
524 <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;"/>
525 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps">
526 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
527 <sanitizer>
528 <valid initial="string.printable">
529 <remove value="'"/>
530 <remove value="&quot;"/>
531 </valid>
532 </sanitizer>
533 </param>
534 </repeat>
535 <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) "/>
536 <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) "/>
537 <param name="param_consensus_blackorwhitelist_use_ppm_tolerance" 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"/>
538 <param name="param_f_and_c_charge" type="text" size="30" value=":" label="Charge range to extract" help="(-charge) ">
539 <sanitizer>
540 <valid initial="string.printable">
541 <remove value="'"/>
542 <remove value="&quot;"/>
543 </valid>
544 </sanitizer>
545 </param>
546 <param name="param_f_and_c_size" type="text" size="30" value=":" label="Size range to extract" help="(-size) ">
547 <sanitizer>
548 <valid initial="string.printable">
549 <remove value="'"/>
550 <remove value="&quot;"/>
551 </valid>
552 </sanitizer>
553 </param>
554 <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta">
555 <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!)!">
556 <sanitizer>
557 <valid initial="string.printable">
558 <remove value="'"/>
559 <remove value="&quot;"/>
560 </valid>
561 </sanitizer>
562 </param>
563 </repeat>
564 <param name="param_id_keep_best_score_id" 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) "/>
565 <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist">
566 <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)">
567 <sanitizer>
568 <valid initial="string.printable">
569 <remove value="'"/>
570 <remove value="&quot;"/>
571 </valid>
572 </sanitizer>
573 </param>
574 </repeat>
575 <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist">
576 <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">
577 <sanitizer>
578 <valid initial="string.printable">
579 <remove value="'"/>
580 <remove value="&quot;"/>
581 </valid>
582 </sanitizer>
583 </param>
584 </repeat>
585 <param name="param_id_remove_annotated_features" type="boolean" truevalue="-id:remove_annotated_features" falsevalue="" checked="false" optional="True" label="Remove features with annotations" help="(-remove_annotated_features) "/>
586 <param name="param_id_remove_unannotated_features" type="boolean" truevalue="-id:remove_unannotated_features" falsevalue="" checked="false" optional="True" label="Remove features without annotations" help="(-remove_unannotated_features) "/>
587 <param name="param_id_remove_unassigned_ids" type="boolean" truevalue="-id:remove_unassigned_ids" falsevalue="" checked="false" optional="True" label="Remove unassigned peptide identifications" help="(-remove_unassigned_ids) "/>
588 <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"/>
589 <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) "/>
590 <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) "/>
591 <param name="param_id_blacklist_imperfect" type="boolean" truevalue="-id:blacklist_imperfect" falsevalue="" checked="false" optional="True" label="Allow for mismatching precursor positions (see 'id:blacklist')" help="(-blacklist_imperfect) "/>
592 <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) "/>
593 <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) "/>
594 <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) "/>
595 <expand macro="advanced_options">
596 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
597 <param name="param_id_remove_clashes" 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) "/>
598 <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"/>
599 <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) "/>
600 <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) "/>
601 <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) "/>
602 <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) "/>
603 </expand>
604 </inputs>
605 <outputs>
606 <data name="param_out" metadata_source="param_in" format="input"/>
607 </outputs>
608 <help>**What it does**
609
610 Extracts or manipulates portions of data from peak, feature or consensus-feature files.
611
612
613 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html</help>
614 <expand macro="references"/>
615 </tool>